8CSS

Human mitochondrial small subunit assembly intermediate (State D)

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2022-05-13 Released: 2022-12-14 
  • Deposition Author(s): Harper, N.J., Burnside, C., Klinge, S.
  • Funding Organization(s): The Robertson Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Principles of mitoribosomal small subunit assembly in eukaryotes.

Harper, N.J.Burnside, C.Klinge, S.

(2023) Nature 614: 175-181

  • DOI: https://doi.org/10.1038/s41586-022-05621-0
  • Primary Citation of Related Structures:  
    8CSP, 8CSQ, 8CSR, 8CSS, 8CST, 8CSU, 8D8J, 8D8K, 8D8L

  • PubMed Abstract: 

    Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism 1 . Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies.


  • Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialA [auth 0]218Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82930 (Homo sapiens)
Explore P82930 
Go to UniProtKB:  P82930
PHAROS:  P82930
GTEx:  ENSG00000074071 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82930
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialB [auth 1]323Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82673 (Homo sapiens)
Explore P82673 
Go to UniProtKB:  P82673
PHAROS:  P82673
GTEx:  ENSG00000061794 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82673
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinC [auth 3]199Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT8 (Homo sapiens)
Explore Q9NWT8 
Go to UniProtKB:  Q9NWT8
PHAROS:  Q9NWT8
GTEx:  ENSG00000175756 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWT8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialD [auth 4]689Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY7 (Homo sapiens)
Explore Q96EY7 
Go to UniProtKB:  Q96EY7
PHAROS:  Q96EY7
GTEx:  ENSG00000132300 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosome-binding factor A, mitochondrialE [auth 6]343Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N0V3 (Homo sapiens)
Explore Q8N0V3 
Go to UniProtKB:  Q8N0V3
PHAROS:  Q8N0V3
GTEx:  ENSG00000101546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N0V3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltransferase-like protein 17, mitochondrialF [auth 7]456Homo sapiensMutation(s): 0 
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7H0 (Homo sapiens)
Explore Q9H7H0 
Go to UniProtKB:  Q9H7H0
PHAROS:  Q9H7H0
GTEx:  ENSG00000165792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7H0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Malonyl-CoA-acyl carrier protein transacylase, mitochondrialG [auth 8]390Homo sapiensMutation(s): 0 
EC: 2.3.1.39
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVS2 (Homo sapiens)
Explore Q8IVS2 
Go to UniProtKB:  Q8IVS2
PHAROS:  Q8IVS2
GTEx:  ENSG00000100294 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IVS2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialI [auth B]296Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y399 (Homo sapiens)
Explore Q9Y399 
Go to UniProtKB:  Q9Y399
PHAROS:  Q9Y399
GTEx:  ENSG00000122140 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y399
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialJ [auth C]167Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EL2 (Homo sapiens)
Explore Q96EL2 
Go to UniProtKB:  Q96EL2
GTEx:  ENSG00000062582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EL2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialK [auth D]430Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82675 (Homo sapiens)
Explore P82675 
Go to UniProtKB:  P82675
PHAROS:  P82675
GTEx:  ENSG00000144029 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82675
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialL [auth E]125Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82932 (Homo sapiens)
Explore P82932 
Go to UniProtKB:  P82932
PHAROS:  P82932
GTEx:  ENSG00000243927 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82932
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialM [auth F]242Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R9 (Homo sapiens)
Explore Q9Y2R9 
Go to UniProtKB:  Q9Y2R9
PHAROS:  Q9Y2R9
GTEx:  ENSG00000125445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2R9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialN [auth G]396Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82933 (Homo sapiens)
Explore P82933 
Go to UniProtKB:  P82933
PHAROS:  P82933
GTEx:  ENSG00000135972 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82933
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialO [auth H]201Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82664 (Homo sapiens)
Explore P82664 
Go to UniProtKB:  P82664
PHAROS:  P82664
GTEx:  ENSG00000048544 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82664
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialP [auth I]194Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82912 (Homo sapiens)
Explore P82912 
Go to UniProtKB:  P82912
PHAROS:  P82912
GTEx:  ENSG00000181991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82912
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialQ [auth J]138Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15235 (Homo sapiens)
Explore O15235 
Go to UniProtKB:  O15235
PHAROS:  O15235
GTEx:  ENSG00000128626 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15235
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialR [auth K]128Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60783 (Homo sapiens)
Explore O60783 
Go to UniProtKB:  O60783
PHAROS:  O60783
GTEx:  ENSG00000120333 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60783
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialS [auth L]257Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82914 (Homo sapiens)
Explore P82914 
Go to UniProtKB:  P82914
PHAROS:  P82914
GTEx:  ENSG00000116898 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82914
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialT [auth M]137Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D3 (Homo sapiens)
Explore Q9Y3D3 
Go to UniProtKB:  Q9Y3D3
PHAROS:  Q9Y3D3
GTEx:  ENSG00000182180 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3D3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialU [auth N]130Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R5 (Homo sapiens)
Explore Q9Y2R5 
Go to UniProtKB:  Q9Y2R5
PHAROS:  Q9Y2R5
GTEx:  ENSG00000239789 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2R5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialV [auth O]258Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y676 (Homo sapiens)
Explore Q9Y676 
Go to UniProtKB:  Q9Y676
PHAROS:  Q9Y676
GTEx:  ENSG00000204568 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y676
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialW [auth P]142Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D5 (Homo sapiens)
Explore Q9Y3D5 
Go to UniProtKB:  Q9Y3D5
PHAROS:  Q9Y3D5
GTEx:  ENSG00000163319 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3D5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialX [auth Q]87Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P82921 (Homo sapiens)
Explore P82921 
Go to UniProtKB:  P82921
PHAROS:  P82921
GTEx:  ENSG00000266472 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82921
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialY [auth R]360Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82650 (Homo sapiens)
Explore P82650 
Go to UniProtKB:  P82650
PHAROS:  P82650
GTEx:  ENSG00000175110 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82650
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialZ [auth S]190Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D9 (Homo sapiens)
Explore Q9Y3D9 
Go to UniProtKB:  Q9Y3D9
PHAROS:  Q9Y3D9
GTEx:  ENSG00000181610 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3D9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialAA [auth T]173Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P82663 (Homo sapiens)
Explore P82663 
Go to UniProtKB:  P82663
PHAROS:  P82663
GTEx:  ENSG00000131368 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82663
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialBA [auth U]205Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYN8 (Homo sapiens)
Explore Q9BYN8 
Go to UniProtKB:  Q9BYN8
GTEx:  ENSG00000125901 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYN8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialCA [auth V]414Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92552 (Homo sapiens)
Explore Q92552 
Go to UniProtKB:  Q92552
PHAROS:  Q92552
GTEx:  ENSG00000113048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92552
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialDA [auth W]187Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Q9 (Homo sapiens)
Explore Q9Y2Q9 
Go to UniProtKB:  Q9Y2Q9
PHAROS:  Q9Y2Q9
GTEx:  ENSG00000147586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2Q9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialEA [auth X]398Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P51398 (Homo sapiens)
Explore P51398 
Go to UniProtKB:  P51398
PHAROS:  P51398
GTEx:  ENSG00000132676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51398
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialFA [auth Y]395Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92665 (Homo sapiens)
Explore Q92665 
Go to UniProtKB:  Q92665
PHAROS:  Q92665
GTEx:  ENSG00000102738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92665
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialGA [auth Z]106Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y291 (Homo sapiens)
Explore Q9Y291 
Go to UniProtKB:  Q9Y291
PHAROS:  Q9Y291
GTEx:  ENSG00000090263 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y291
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains LengthOrganismImage
12S mitochondrial rRNAH [auth A]955Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
UB [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ATP
Query on ATP

Download Ideal Coordinates CCD File 
ZB [auth X]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
BC [auth X]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
IA [auth 7]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
HA [auth 7]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
XB [auth P],
YB [auth T]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
WB [auth O]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
JA [auth A]
KA [auth A]
LA [auth A]
MA [auth A]
NA [auth A]
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth X]
BB [auth A]
CB [auth A]
DB [auth A]
AB [auth A],
AC [auth X],
BB [auth A],
CB [auth A],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth A],
HB [auth A],
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
MB [auth A],
NB [auth A],
OB [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
TA [auth A],
TB [auth A],
UA [auth A],
VA [auth A],
VB [auth B],
WA [auth A],
XA [auth A],
YA [auth A],
ZA [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
X [auth Q]L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONPHENIX1.19

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Robertson Foundation--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM136640-02

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references