7K3V | pdb_00007k3v

Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV Titan Krios G3i electron microscope with K3 detector

• PDB DOI: https://doi.org/10.2210/pdb7K3V/pdb
• EM Map EMD-22657: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-09-14 Released: 2020-11-18 
• Deposition Author(s): Zhang, K., Pintilie, G., Li, S., Schmid, M., Chiu, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Resolving individual atoms of protein complex by cryo-electron microscopy.

Zhang, K., Pintilie, G.D., Li, S., Schmid, M.F., Chiu, W.

(2020) Cell Res 30: 1136-1139

• PubMed: 33139928 
• DOI: https://doi.org/10.1038/s41422-020-00432-2
• Primary Citation Related Structures: 
  7K3V, 7K3W, 7RRP

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Organizational Affiliation: 
• Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA. [e-mail].
Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA.
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA.
Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA. [e-mail].
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 501.25 kDa 
• Atom Count: 38,406 
• Modeled Residue Count: 4,128 
• Deposited Residue Count: 4,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	172	Homo sapiens	Mutation(s): 0  Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens) Explore P02794  Go to UniProtKB:  P02794
PHAROS:  P02794 GTEx:  ENSG00000167996

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AA [auth A], AD [auth F], AE [auth H], AG [auth L], AI [auth O], AJ [auth Q], AK [auth S], AL [auth U], BA [auth A], BB [auth B], BC [auth D], BD [auth F], BF [auth J], BG [auth L], BH [auth M], BJ [auth Q], BK [auth S], BL [auth U], BM [auth W], CA [auth A], CB [auth C], CC [auth D], CD [auth F], CE [auth H], CF [auth J], CG [auth L], CI [auth O], CJ [auth Q], CK [auth S], CL [auth U], CM [auth W], DB [auth C], DC [auth D], DD [auth F], DE [auth H], DG [auth L], DI [auth P], DJ [auth Q], DK [auth S], DL [auth U], DM [auth W], EA [auth A], EB [auth C], ED [auth F], EE [auth H], EF [auth J], EH [auth N], EI [auth P], EJ [auth R], EK [auth S], EL [auth U], EM [auth W], FA [auth A], FB [auth C], FC [auth D], FD [auth F], FF [auth J], FG [auth L], FH [auth N], FJ [auth R], FK [auth T], FL [auth U], FM [auth W], GA [auth A], GB [auth C], GC [auth E], GD [auth F], GE [auth H], GF [auth J], GG [auth L], GI [auth P], GM [auth W], HC [auth E], HD [auth F], HE [auth H], HF [auth J], HG [auth L], HH [auth N], HI [auth P], HJ [auth R], HK [auth T], HL [auth V], HM [auth X], IA [auth A], IB [auth C], IC [auth E], IE [auth H], IF [auth J], IH [auth N], IK [auth T], IL [auth V], IM [auth X], JA [auth A], JB [auth C], JC [auth E], JD [auth G], JF [auth J], JG [auth L], JH [auth N], JJ [auth R], JL [auth V], KA [auth A], KB [auth C], KD [auth G], KE [auth H], KF [auth J], KG [auth L], KH [auth N], KI [auth P], KK [auth T], KM [auth X], LC [auth E], LD [auth G], LE [auth I], LF [auth J], LG [auth L], LH [auth N], LI [auth P], LL [auth V], LM [auth X], MA [auth A], MB [auth C], MC [auth E], MD [auth G], ME [auth I], MH [auth N], MI [auth P], MJ [auth R], NA [auth B], NB [auth C], NC [auth E], ND [auth G], NE [auth I], NF [auth K], NG [auth L], NH [auth N], NI [auth P], NJ [auth R], NK [auth T], OA [auth B], OB [auth C], OE [auth I], OF [auth K], OH [auth N], OI [auth P], OJ [auth R], OK [auth T], OL [auth V], OM [auth X], PA [auth B], PC [auth E], PD [auth G], PF [auth K], PG [auth M], PH [auth O], PI [auth P], PJ [auth R], PK [auth T], PL [auth V], PM [auth X], QA [auth B], QB [auth C], QC [auth E], QD [auth G], QE [auth I], QF [auth K], QG [auth M], QI [auth Q], QJ [auth R], QK [auth T], QL [auth V], QM [auth X], RA [auth B], RB [auth D], RC [auth E], RE [auth I], RF [auth K], RG [auth M], RH [auth O], RJ [auth R], RK [auth T], RL [auth V], RM [auth X], SB [auth D], SD [auth G], SE [auth I], SG [auth M], SH [auth O], SI [auth Q], SJ [auth S], SK [auth T], SL [auth V], SM [auth X], TA [auth B], TB [auth D], TC [auth E], TD [auth G], TF [auth K], TG [auth M], TH [auth O], TI [auth Q], TJ [auth S], TK [auth U], TL [auth V], TM [auth X], UA [auth B], UB [auth D], UE [auth I], UF [auth K], UH [auth O], UK [auth U], UL [auth W], VA [auth B], VB [auth D], VD [auth G], VE [auth I], VG [auth M], VI [auth Q], VJ [auth S], VL [auth W], WC [auth F], WD [auth H], WE [auth I], WF [auth K], WG [auth M], WH [auth O], WJ [auth S], WK [auth U], XA [auth B], XB [auth D], XC [auth F], XD [auth H], XF [auth K], XH [auth O], XK [auth U], XL [auth W], Y [auth A], YA [auth B], YB [auth D], YD [auth H], YE [auth I], YG [auth M], YI [auth Q], YL [auth W], Z [auth A], ZA [auth B], ZB [auth D], ZC [auth F], ZD [auth H], ZF [auth K], ZG [auth M], ZH [auth O], ZI [auth Q], ZJ [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	AB [auth B], AC [auth D], AF [auth J], AH [auth M], AM [auth W], BE [auth H], BI [auth O], CH [auth N], DA [auth A], DF [auth J], DH [auth N], EC [auth D], EG [auth L], FE [auth H], FI [auth P], GH [auth N], GJ [auth R], GK [auth T], GL [auth V], HA [auth A], HB [auth C], ID [auth G], IG [auth L], II [auth P], IJ [auth R], JE [auth H], JI [auth P], JK [auth T], JM [auth X], KC [auth E], KJ [auth R], KL [auth V], LA [auth A], LB [auth C], LJ [auth R], LK [auth T], MF [auth K], MG [auth L], MK [auth T], ML [auth V], MM [auth X], NL [auth V], NM [auth X], OC [auth E], OD [auth G], OG [auth M], PB [auth C], PE [auth I], QH [auth O], RD [auth G], RI [auth Q], SA [auth B], SC [auth E], SF [auth K], TE [auth I], UC [auth F], UD [auth G], UG [auth M], UI [auth Q], UJ [auth S], VC [auth F], VF [auth K], VH [auth O], VK [auth U], WA [auth B], WB [auth D], WI [auth Q], WL [auth W], XE [auth I], XG [auth M], XI [auth Q], XJ [auth S], YC [auth F], YF [auth K], YH [auth O], YJ [auth S], YK [auth U], ZE [auth J], ZK [auth U], ZL [auth W]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.18.2_3874

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Zhang, K., Pintilie, G., Li, S., Schmid, M., Chiu, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM129564
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM079429
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103832

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Data collection, Refinement description
• Version 1.2: 2020-12-23
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Refinement description