8HTU | pdb_00008htu

Cryo-EM structure of PpPSI-L


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history

Literature

Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens.

Sun, H.Shang, H.Pan, X.Li, M.

(2023) Nat Plants 9: 1347-1358

  • DOI: https://doi.org/10.1038/s41477-023-01463-4
  • Primary Citation Related Structures: 
    8HTU

  • PubMed Abstract: 

    In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss Physcomitrium patens (P. patens) represents a well-studied primary land-dwelling photosynthetic autotroph branching from the common ancestor of green algae and land plants at the early stage of evolution. P. patens possesses at least three types of PSI with different antenna sizes. The largest PSI form (PpPSI-L) exhibits a unique organization found neither in flowering plants nor in algae. Its formation is mediated by the P. patens-specific LHC protein, Lhcb9. While previous studies have revealed the overall architecture of PpPSI-L, its assembly details and the relationship between different PpPSI types remain unclear. Here we report the high-resolution structure of PpPSI-L. We identified 14 PSI core subunits, one Lhcb9, one phosphorylated LHCII trimer and eight LHCI monomers arranged as two belts. Our structural analysis established the essential role of Lhcb9 and the phosphorylated LHCII in stabilizing the complex. In addition, our results suggest that PpPSI switches between different types, which share identical modules. This feature may contribute to the dynamic adjustment of the light-harvesting capability of PSI under different light conditions.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 985.79 kDa 
  • Atom Count: 57,715 
  • Modeled Residue Count: 5,089 
  • Deposited Residue Count: 6,382 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth U],
B [auth V],
C [auth W]
265Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9RT62 (Physcomitrium patens)
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UniProt GroupA9RT62
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticD [auth 1],
V [auth 5]
245Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JLZ3 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticE [auth 2],
W [auth 6]
273Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9TJ06 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticF [auth 3],
X [auth 7]
323Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IB10 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticG [auth 4],
Y [auth 8]
270Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1K0E4 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1H [auth A]750Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q8MFA3 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2I [auth B]734Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q8MFA2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerJ [auth C]81Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXQ2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticK [auth D]210Physcomitrium patensMutation(s): 0 
UniProt
Find proteins for A9REG3 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplasticL [auth E]132Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IHL7 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIM [auth F]246Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IN36 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticN [auth G]155Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JC42 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplasticO [auth H]139Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JDR4 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIP [auth I]36Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXR3 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXQ [auth J]41Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXM2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit XR [auth K]132Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1KU02 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI subunit VS [auth L]223Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A7I4A0Q6 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIT [auth M]32Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXK4 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit OU [auth O]143Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A7I4AUU1 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticZ [auth 9]311Physcomitrium patensMutation(s): 0 
UniProt
Find proteins for A0A2K1KKR9 (Physcomitrium patens)
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
CJ [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



Download:Ideal Coordinates CCD File
AA [auth U]
AB [auth V]
BB [auth V]
BD [auth 2]
CD [auth 2]
AA [auth U],
AB [auth V],
BB [auth V],
BD [auth 2],
CD [auth 2],
DD [auth 2],
EA [auth U],
EM [auth 7],
FA [auth U],
FC [auth 1],
FN [auth 8],
GA [auth U],
HA [auth U],
HL [auth 6],
IA [auth U],
IL [auth 6],
KC [auth 1],
KD [auth 2],
KN [auth 9],
LL [auth 6],
MB [auth W],
ML [auth 6],
NE [auth 4],
NL [auth 6],
OE [auth 4],
ON [auth 9],
PE [auth 4],
PN [auth 9],
QB [auth W],
QK [auth 5],
QN [auth 9],
RB [auth W],
RN [auth 9],
SB [auth W],
TA [auth V],
TB [auth W],
UB [auth W],
UL [auth 6],
VD [auth 3],
VK [auth 5],
WE [auth 4],
WM [auth 8],
XA [auth V],
XC [auth 2],
XM [auth 8],
YA [auth V],
YC [auth 2],
YM [auth 8],
ZA [auth V]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AD [auth 2]
AE [auth 3]
AG [auth A]
AI [auth B]
AK [auth K]
AD [auth 2],
AE [auth 3],
AG [auth A],
AI [auth B],
AK [auth K],
AL [auth 5],
AM [auth 7],
AN [auth 8],
BA [auth U],
BE [auth 3],
BF [auth A],
BG [auth A],
BI [auth B],
BL [auth 5],
BM [auth 7],
BN [auth 8],
CA [auth U],
CB [auth V],
CE [auth 3],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth B],
CK [auth K],
CL [auth 5],
CM [auth 7],
CN [auth 8],
DA [auth U],
DB [auth V],
DE [auth 3],
DF [auth A],
DG [auth A],
DI [auth B],
DL [auth 5],
DM [auth 7],
DN [auth 8],
EB [auth V],
ED [auth 2],
EF [auth A],
EG [auth A],
EI [auth B],
EN [auth 8],
FB [auth V],
FD [auth 2],
FF [auth A],
FG [auth A],
FI [auth B],
FK [auth L],
FM [auth 7],
GB [auth V],
GC [auth 1],
GD [auth 2],
GF [auth A],
GG [auth A],
GI [auth B],
GK [auth L],
GM [auth 7],
HC [auth 1],
HD [auth 2],
HF [auth A],
HG [auth A],
HH [auth B],
HI [auth B],
HJ [auth F],
HK [auth L],
HM [auth 7],
IC [auth 1],
ID [auth 2],
IF [auth A],
IG [auth A],
IH [auth B],
II [auth B],
IJ [auth F],
IM [auth 7],
JA [auth U],
JC [auth 1],
JD [auth 2],
JE [auth 4],
JF [auth A],
JG [auth A],
JH [auth B],
JI [auth B],
JJ [auth F],
JL [auth 6],
JM [auth 7],
KA [auth U],
KE [auth 4],
KF [auth A],
KG [auth A],
KH [auth B],
KI [auth B],
KL [auth 6],
KM [auth 7],
LA [auth U],
LC [auth 1],
LE [auth 4],
LF [auth A],
LG [auth A],
LH [auth B],
LI [auth B],
LJ [auth G],
LM [auth 7],
LN [auth 9],
MA [auth U],
MC [auth 1],
ME [auth 4],
MF [auth A],
MG [auth A],
MH [auth B],
MI [auth B],
MK [auth O],
MM [auth 7],
MN [auth 9],
NA [auth U],
NB [auth W],
NC [auth 1],
NF [auth A],
NG [auth A],
NH [auth B],
NI [auth B],
NJ [auth G],
NK [auth O],
NN [auth 9],
OB [auth W],
OC [auth 1],
OF [auth A],
OG [auth A],
OH [auth B],
OI [auth B],
OJ [auth G],
OK [auth O],
OL [auth 6],
PB [auth W],
PC [auth 1],
PF [auth A],
PG [auth A],
PH [auth B],
PI [auth B],
PL [auth 6],
QC [auth 1],
QD [auth 3],
QE [auth 4],
QF [auth A],
QG [auth A],
QH [auth B],
QI [auth B],
QL [auth 6],
RC [auth 1],
RD [auth 3],
RE [auth 4],
RF [auth A],
RG [auth A],
RH [auth B],
RI [auth B],
RJ [auth H],
RK [auth 5],
RL [auth 6],
SC [auth 1],
SD [auth 3],
SE [auth 4],
SF [auth A],
SH [auth B],
SI [auth B],
SK [auth 5],
SL [auth 6],
SM [auth 8],
SN [auth 9],
TD [auth 3],
TE [auth 4],
TF [auth A],
TG [auth A],
TH [auth B],
TI [auth B],
TJ [auth J],
TK [auth 5],
TL [auth 6],
TM [auth 8],
TN [auth 9],
UA [auth V],
UD [auth 3],
UE [auth 4],
UF [auth A],
UH [auth B],
UI [auth B],
UK [auth 5],
UM [auth 8],
UN [auth 9],
VA [auth V],
VB [auth W],
VE [auth 4],
VF [auth A],
VH [auth B],
VM [auth 8],
VN [auth 9],
WA [auth V],
WB [auth W],
WD [auth 3],
WF [auth A],
WH [auth B],
WK [auth 5],
WN [auth 9],
XB [auth W],
XD [auth 3],
XF [auth A],
XH [auth B],
XJ [auth K],
XK [auth 5],
YB [auth W],
YD [auth 3],
YF [auth A],
YH [auth B],
YK [auth 5],
ZB [auth W],
ZC [auth 2],
ZD [auth 3],
ZF [auth A],
ZH [auth B],
ZJ [auth K],
ZK [auth 5],
ZL [auth 7],
ZM [auth 8]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
FH [auth A]
KK [auth L]
MJ [auth G]
PD [auth 2]
VJ [auth J]
FH [auth A],
KK [auth L],
MJ [auth G],
PD [auth 2],
VJ [auth J],
WJ [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



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AF [auth 4]
BO [auth 9]
DJ [auth B]
EC [auth W]
GL [auth 5]
AF [auth 4],
BO [auth 9],
DJ [auth B],
EC [auth W],
GL [auth 5],
IE [auth 3],
JN [auth 8],
LB [auth V],
OD [auth 2],
RM [auth 7],
SA [auth U],
UG [auth A],
VG [auth A],
WC [auth 1],
YL [auth 6]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX

Query on NEX



Download:Ideal Coordinates CCD File
DC [auth W],
KB [auth V],
RA [auth U],
ZN [auth 9]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT

Query on XAT



Download:Ideal Coordinates CCD File
CC [auth W]
FE [auth 3]
FL [auth 5]
HN [auth 8]
JB [auth V]
CC [auth W],
FE [auth 3],
FL [auth 5],
HN [auth 8],
JB [auth V],
MD [auth 2],
OM [auth 7],
QA [auth U],
UC [auth 1],
WL [auth 6],
YE [auth 4]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT

Query on LUT



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AC [auth W]
AO [auth 9]
BC [auth W]
EE [auth 3]
EL [auth 5]
AC [auth W],
AO [auth 9],
BC [auth W],
EE [auth 3],
EL [auth 5],
GN [auth 8],
HB [auth V],
IB [auth V],
LD [auth 2],
NM [auth 7],
OA [auth U],
PA [auth U],
TC [auth 1],
VL [auth 6],
XE [auth 4],
XN [auth 9],
YN [auth 9]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR

Query on BCR



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AH [auth A]
AJ [auth B]
BK [auth K]
DH [auth A]
EJ [auth B]
AH [auth A],
AJ [auth B],
BK [auth K],
DH [auth A],
EJ [auth B],
EK [auth L],
GE [auth 3],
GH [auth B],
HE [auth 3],
IK [auth L],
IN [auth 8],
JK [auth L],
KJ [auth F],
LK [auth M],
ND [auth 2],
PJ [auth G],
PK [auth O],
PM [auth 7],
QM [auth 7],
SJ [auth I],
UJ [auth J],
VC [auth 1],
WG [auth A],
WI [auth B],
XG [auth A],
XI [auth B],
XL [auth 6],
YG [auth A],
YI [auth B],
YJ [auth K],
ZE [auth 4],
ZG [auth A],
ZI [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BJ [auth B],
DK [auth K],
EH [auth A],
QJ [auth G]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN



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SG [auth A],
VI [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
BH [auth A],
FJ [auth C],
GJ [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A [auth U],
B [auth V],
C [auth W]
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary