8QU1

mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1

• PDB DOI: https://doi.org/10.2210/pdb8QU1/pdb
• EM Map EMD-18460: EMDB EMDataResource

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


• Deposited: 2023-10-13 Released: 2024-06-26 
• Deposition Author(s): Valentin Gese, G., Cipullo, M., Rorbach, J., Hallberg, B.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

GTPBP8 plays a role in mitoribosome formation in human mitochondria

Cipullo, M., Valentin Gese, G., Gopalakrishna, S., Krueger, A., Lobo, V., Pirozhkova, M.A., Marks, J., Palenkova, P., Shiriaev, D., Liu, Y., Misic, J., Cai, Y., Nguyen, M., Abdelbagi, A., Li, X., Minczuk, M., Hafner, M., Benhalevy, D., Sarshad, A.A., Attanasov, I., Hallberg, B.M., Rorbach, J.

(2024) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 28-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,237.16 kDa 
• Atom Count: 57,235 
• Modelled Residue Count: 5,429 
• Deposited Residue Count: 7,909 
• Unique protein chains: 28
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L2, mitochondrial	C [auth D]	305	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T653 (Homo sapiens) Explore Q5T653  Go to UniProtKB:  Q5T653
PHAROS:  Q5T653 GTEx:  ENSG00000112651

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L3, mitochondrial	D [auth E]	348	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09001 (Homo sapiens) Explore P09001  Go to UniProtKB:  P09001
PHAROS:  P09001 GTEx:  ENSG00000114686

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L4, mitochondrial	E [auth F]	311	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYD3 (Homo sapiens) Explore Q9BYD3  Go to UniProtKB:  Q9BYD3
PHAROS:  Q9BYD3 GTEx:  ENSG00000105364

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L9, mitochondrial	F [auth H]	267	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYD2 (Homo sapiens) Explore Q9BYD2  Go to UniProtKB:  Q9BYD2
PHAROS:  Q9BYD2 GTEx:  ENSG00000143436

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L10, mitochondrial	G [auth I]	261	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7H8 (Homo sapiens) Explore Q7Z7H8  Go to UniProtKB:  Q7Z7H8
PHAROS:  Q7Z7H8 GTEx:  ENSG00000159111

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L11, mitochondrial	H [auth J]	192	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3B7 (Homo sapiens) Explore Q9Y3B7  Go to UniProtKB:  Q9Y3B7
PHAROS:  Q9Y3B7 GTEx:  ENSG00000174547

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L13, mitochondrial	I [auth K]	178	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYD1 (Homo sapiens) Explore Q9BYD1  Go to UniProtKB:  Q9BYD1
PHAROS:  Q9BYD1 GTEx:  ENSG00000172172

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L14, mitochondrial	J [auth L]	145	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P1L8 (Homo sapiens) Explore Q6P1L8  Go to UniProtKB:  Q6P1L8
PHAROS:  Q6P1L8 GTEx:  ENSG00000180992

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L15, mitochondrial	K [auth M]	296	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P015 (Homo sapiens) Explore Q9P015  Go to UniProtKB:  Q9P015
PHAROS:  Q9P015 GTEx:  ENSG00000137547

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L16, mitochondrial	L [auth N]	251	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX20 (Homo sapiens) Explore Q9NX20  Go to UniProtKB:  Q9NX20
PHAROS:  Q9NX20 GTEx:  ENSG00000166902

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L17, mitochondrial	M [auth O]	175	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRX2 (Homo sapiens) Explore Q9NRX2  Go to UniProtKB:  Q9NRX2
PHAROS:  Q9NRX2 GTEx:  ENSG00000158042

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L18, mitochondrial	N [auth P]	180	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0U6 (Homo sapiens) Explore Q9H0U6  Go to UniProtKB:  Q9H0U6
PHAROS:  Q9H0U6 GTEx:  ENSG00000112110

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L19, mitochondrial	O [auth Q]	292	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49406 (Homo sapiens) Explore P49406  Go to UniProtKB:  P49406
PHAROS:  P49406 GTEx:  ENSG00000115364

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L20, mitochondrial	P [auth R]	149	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYC9 (Homo sapiens) Explore Q9BYC9  Go to UniProtKB:  Q9BYC9
PHAROS:  Q9BYC9 GTEx:  ENSG00000242485

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L21, mitochondrial	Q [auth S]	205	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z2W9 (Homo sapiens) Explore Q7Z2W9  Go to UniProtKB:  Q7Z2W9
GTEx:  ENSG00000197345

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L22, mitochondrial	R [auth T]	206	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWU5 (Homo sapiens) Explore Q9NWU5  Go to UniProtKB:  Q9NWU5
PHAROS:  Q9NWU5 GTEx:  ENSG00000082515

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L23, mitochondrial	S [auth U]	153	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16540 (Homo sapiens) Explore Q16540  Go to UniProtKB:  Q16540
PHAROS:  Q16540 GTEx:  ENSG00000214026

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L24, mitochondrial	T [auth V]	216	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96A35 (Homo sapiens) Explore Q96A35  Go to UniProtKB:  Q96A35
PHAROS:  Q96A35 GTEx:  ENSG00000143314

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L27, mitochondrial	U [auth W]	148	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0M9 (Homo sapiens) Explore Q9P0M9  Go to UniProtKB:  Q9P0M9
PHAROS:  Q9P0M9 GTEx:  ENSG00000108826

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L28, mitochondrial	V [auth X]	256	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13084 (Homo sapiens) Explore Q13084  Go to UniProtKB:  Q13084
PHAROS:  Q13084 GTEx:  ENSG00000086504

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L47, mitochondrial	W [auth Y]	250	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD33 (Homo sapiens) Explore Q9HD33  Go to UniProtKB:  Q9HD33
PHAROS:  Q9HD33 GTEx:  ENSG00000136522

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L30, mitochondrial	X [auth Z]	161	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCC3 (Homo sapiens) Explore Q8TCC3  Go to UniProtKB:  Q8TCC3
PHAROS:  Q8TCC3 GTEx:  ENSG00000185414

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L32, mitochondrial	Y [auth 0]	188	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYC8 (Homo sapiens) Explore Q9BYC8  Go to UniProtKB:  Q9BYC8
PHAROS:  Q9BYC8 GTEx:  ENSG00000106591

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L33, mitochondrial	Z [auth 1]	65	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75394 (Homo sapiens) Explore O75394  Go to UniProtKB:  O75394
PHAROS:  O75394 GTEx:  ENSG00000243147

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L34, mitochondrial	AA [auth 2]	92	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQ48 (Homo sapiens) Explore Q9BQ48  Go to UniProtKB:  Q9BQ48
PHAROS:  Q9BQ48 GTEx:  ENSG00000130312

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L35, mitochondrial	BA [auth 3]	188	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZE8 (Homo sapiens) Explore Q9NZE8  Go to UniProtKB:  Q9NZE8
PHAROS:  Q9NZE8 GTEx:  ENSG00000132313

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L37, mitochondrial	CA [auth 5]	423	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZE1 (Homo sapiens) Explore Q9BZE1  Go to UniProtKB:  Q9BZE1
PHAROS:  Q9BZE1 GTEx:  ENSG00000116221

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
39S ribosomal protein L38, mitochondrial	DA [auth 6]	380	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DV4 (Homo sapiens) Explore Q96DV4  Go to UniProtKB:  Q96DV4
GTEx:  ENSG00000204316

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A	1,559	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
mitochondrial tRNAVal	B	69	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Valentin Gese, G., Cipullo, M., Rorbach, J., Hallberg, B.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release