7CK8 | pdb_00007ck8

Crystal structure of human ferritin heavy chain mutant C90S/C102S/C130S

PDB DOI: https://doi.org/10.2210/pdb7CK8/pdb

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-07-16 Released: 2021-05-26
Deposition Author(s): Chen, X., Jiang, B., Yan, X., Fan, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.225 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A natural drug entry channel in the ferritin nanocage.

Jiang, B., Chen, X., Sun, G., Chen, X., Yin, Y., Jin, Y., Mi, Q., Ma, L., Yang, Y., Yan, X., Fan, K.

(2020) Nano Today 35

DOI: https://doi.org/10.1016/j.nantod.2020.100948

Macromolecule Content

Total Structure Weight: 245.25 kDa
Atom Count: 22,459
Modeled Residue Count: 2,069
Deposited Residue Count: 2,076
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	173	Homo sapiens	Mutation(s): 3 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02794
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain UA [auth D] SDF format, chain S [auth A] SDF format, chain MC [auth I] SDF format, chain HA [auth C] SDF format, chain BB [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain MC [auth I] MOL2 format, chain HA [auth C] MOL2 format, chain BB [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain MC [auth I] mmCIF format, chain HA [auth C] mmCIF format, chain BB [auth E]	AA [auth B] BB [auth E] HA [auth C] MC [auth I] S [auth A] AA [auth B], BB [auth E], HA [auth C], MC [auth I], S [auth A], UA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BB [auth E] Focus chain HA [auth C] Focus chain MC [auth I] Focus chain S [auth A] Focus chain UA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BB [auth E] Focus chain HA [auth C] Focus chain MC [auth I] Focus chain S [auth A] Focus chain UA [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain TA [auth D] MOL2 format, chain TA [auth D] mmCIF format, chain TA [auth D]	TA [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain TA [auth D] Interactions & Density Focus chain TA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain OA [auth D] SDF format, chain VB [auth H] SDF format, chain ZC [auth L] SDF format, chain YA [auth E] SDF format, chain XB [auth H] SDF format, chain XA [auth E] SDF format, chain X [auth B] SDF format, chain WC [auth K] SDF format, chain WB [auth H] SDF format, chain WA [auth E] SDF format, chain W [auth B] SDF format, chain VC [auth K] SDF format, chain V [auth B] SDF format, chain UC [auth K] SDF format, chain U [auth B] SDF format, chain RC [auth J] SDF format, chain QC [auth J] SDF format, chain QA [auth D] SDF format, chain PC [auth J] SDF format, chain PB [auth G] SDF format, chain PA [auth D] SDF format, chain OB [auth G] SDF format, chain O [auth A] SDF format, chain NB [auth G] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MB [auth G] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain IC [auth I] SDF format, chain IB [auth F] SDF format, chain HC [auth I] SDF format, chain HB [auth F] SDF format, chain GC [auth I] SDF format, chain GB [auth F] SDF format, chain FC [auth I] SDF format, chain FB [auth F] SDF format, chain EC [auth I] SDF format, chain EB [auth F] SDF format, chain EA [auth C] SDF format, chain DC [auth I] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain AD [auth L] MOL2 format, chain OA [auth D] MOL2 format, chain VB [auth H] MOL2 format, chain ZC [auth L] MOL2 format, chain YA [auth E] MOL2 format, chain XB [auth H] MOL2 format, chain XA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain WC [auth K] MOL2 format, chain WB [auth H] MOL2 format, chain WA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain VC [auth K] MOL2 format, chain V [auth B] MOL2 format, chain UC [auth K] MOL2 format, chain U [auth B] MOL2 format, chain RC [auth J] MOL2 format, chain QC [auth J] MOL2 format, chain QA [auth D] MOL2 format, chain PC [auth J] MOL2 format, chain PB [auth G] MOL2 format, chain PA [auth D] MOL2 format, chain OB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth G] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain IC [auth I] MOL2 format, chain IB [auth F] MOL2 format, chain HC [auth I] MOL2 format, chain HB [auth F] MOL2 format, chain GC [auth I] MOL2 format, chain GB [auth F] MOL2 format, chain FC [auth I] MOL2 format, chain FB [auth F] MOL2 format, chain EC [auth I] MOL2 format, chain EB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain DC [auth I] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain AD [auth L] mmCIF format, chain OA [auth D] mmCIF format, chain VB [auth H] mmCIF format, chain ZC [auth L] mmCIF format, chain YA [auth E] mmCIF format, chain XB [auth H] mmCIF format, chain XA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain WC [auth K] mmCIF format, chain WB [auth H] mmCIF format, chain WA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain VC [auth K] mmCIF format, chain V [auth B] mmCIF format, chain UC [auth K] mmCIF format, chain U [auth B] mmCIF format, chain RC [auth J] mmCIF format, chain QC [auth J] mmCIF format, chain QA [auth D] mmCIF format, chain PC [auth J] mmCIF format, chain PB [auth G] mmCIF format, chain PA [auth D] mmCIF format, chain OB [auth G] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth G] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth G] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain IC [auth I] mmCIF format, chain IB [auth F] mmCIF format, chain HC [auth I] mmCIF format, chain HB [auth F] mmCIF format, chain GC [auth I] mmCIF format, chain GB [auth F] mmCIF format, chain FC [auth I] mmCIF format, chain FB [auth F] mmCIF format, chain EC [auth I] mmCIF format, chain EB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain DC [auth I] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain AD [auth L]	AD [auth L] CA [auth C] DA [auth C] DC [auth I] EA [auth C] AD [auth L], CA [auth C], DA [auth C], DC [auth I], EA [auth C], EB [auth F], EC [auth I], FB [auth F], FC [auth I], GB [auth F], GC [auth I], HB [auth F], HC [auth I], IB [auth F], IC [auth I], LA [auth D], M [auth A], MA [auth D], MB [auth G], N [auth A], NA [auth D], NB [auth G], O [auth A], OA [auth D], OB [auth G], PA [auth D], PB [auth G], PC [auth J], QA [auth D], QC [auth J], RC [auth J], U [auth B], UC [auth K], V [auth B], VB [auth H], VC [auth K], W [auth B], WA [auth E], WB [auth H], WC [auth K], X [auth B], XA [auth E], XB [auth H], YA [auth E], ZC [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AD [auth L] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DC [auth I] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain EC [auth I] Focus chain FB [auth F] Focus chain FC [auth I] Focus chain GB [auth F] Focus chain GC [auth I] Focus chain HB [auth F] Focus chain HC [auth I] Focus chain IB [auth F] Focus chain IC [auth I] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain PC [auth J] Focus chain QA [auth D] Focus chain QC [auth J] Focus chain RC [auth J] Focus chain U [auth B] Focus chain UC [auth K] Focus chain V [auth B] Focus chain VB [auth H] Focus chain VC [auth K] Focus chain W [auth B] Focus chain WA [auth E] Focus chain WB [auth H] Focus chain WC [auth K] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth H] Focus chain YA [auth E] Focus chain ZC [auth L] Interactions & Density Focus chain AD [auth L] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DC [auth I] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain EC [auth I] Focus chain FB [auth F] Focus chain FC [auth I] Focus chain GB [auth F] Focus chain GC [auth I] Focus chain HB [auth F] Focus chain HC [auth I] Focus chain IB [auth F] Focus chain IC [auth I] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain PC [auth J] Focus chain QA [auth D] Focus chain QC [auth J] Focus chain RC [auth J] Focus chain U [auth B] Focus chain UC [auth K] Focus chain V [auth B] Focus chain VB [auth H] Focus chain VC [auth K] Focus chain W [auth B] Focus chain WA [auth E] Focus chain WB [auth H] Focus chain WC [auth K] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth H] Focus chain YA [auth E] Focus chain ZC [auth L]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain DD [auth L] SDF format, chain UB [auth G] SDF format, chain VA [auth D] SDF format, chain TB [auth G] SDF format, chain T [auth A] SDF format, chain OC [auth I] SDF format, chain NC [auth I] SDF format, chain LB [auth F] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain DB [auth E] SDF format, chain CC [auth H] SDF format, chain CB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain DD [auth L] MOL2 format, chain UB [auth G] MOL2 format, chain VA [auth D] MOL2 format, chain TB [auth G] MOL2 format, chain T [auth A] MOL2 format, chain OC [auth I] MOL2 format, chain NC [auth I] MOL2 format, chain LB [auth F] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain DB [auth E] MOL2 format, chain CC [auth H] MOL2 format, chain CB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain DD [auth L] mmCIF format, chain UB [auth G] mmCIF format, chain VA [auth D] mmCIF format, chain TB [auth G] mmCIF format, chain T [auth A] mmCIF format, chain OC [auth I] mmCIF format, chain NC [auth I] mmCIF format, chain LB [auth F] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain DB [auth E] mmCIF format, chain CC [auth H] mmCIF format, chain CB [auth E]	BA [auth B] CB [auth E] CC [auth H] DB [auth E] DD [auth L] BA [auth B], CB [auth E], CC [auth H], DB [auth E], DD [auth L], IA [auth C], JA [auth C], KA [auth C], LB [auth F], NC [auth I], OC [auth I], T [auth A], TB [auth G], UB [auth G], VA [auth D]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CB [auth E] Focus chain CC [auth H] Focus chain DB [auth E] Focus chain DD [auth L] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LB [auth F] Focus chain NC [auth I] Focus chain OC [auth I] Focus chain T [auth A] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain VA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CB [auth E] Focus chain CC [auth H] Focus chain DB [auth E] Focus chain DD [auth L] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LB [auth F] Focus chain NC [auth I] Focus chain OC [auth I] Focus chain T [auth A] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain VA [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain ZB [auth H] SDF format, chain ZA [auth E] SDF format, chain Z [auth B] SDF format, chain YC [auth K] SDF format, chain YB [auth H] SDF format, chain Y [auth B] SDF format, chain XC [auth K] SDF format, chain TC [auth J] SDF format, chain SC [auth J] SDF format, chain SB [auth G] SDF format, chain SA [auth D] SDF format, chain RB [auth G] SDF format, chain RA [auth D] SDF format, chain R [auth A] SDF format, chain QB [auth G] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain LC [auth I] SDF format, chain KC [auth I] SDF format, chain KB [auth F] SDF format, chain JC [auth I] SDF format, chain JB [auth F] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain CD [auth L] SDF format, chain BD [auth L] SDF format, chain BC [auth H] SDF format, chain AC [auth H] SDF format, chain AB [auth E] MOL2 format, chain ZB [auth H] MOL2 format, chain ZA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain YC [auth K] MOL2 format, chain YB [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain XC [auth K] MOL2 format, chain TC [auth J] MOL2 format, chain SC [auth J] MOL2 format, chain SB [auth G] MOL2 format, chain SA [auth D] MOL2 format, chain RB [auth G] MOL2 format, chain RA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain LC [auth I] MOL2 format, chain KC [auth I] MOL2 format, chain KB [auth F] MOL2 format, chain JC [auth I] MOL2 format, chain JB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain CD [auth L] MOL2 format, chain BD [auth L] MOL2 format, chain BC [auth H] MOL2 format, chain AC [auth H] MOL2 format, chain AB [auth E] mmCIF format, chain ZB [auth H] mmCIF format, chain ZA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain YC [auth K] mmCIF format, chain YB [auth H] mmCIF format, chain Y [auth B] mmCIF format, chain XC [auth K] mmCIF format, chain TC [auth J] mmCIF format, chain SC [auth J] mmCIF format, chain SB [auth G] mmCIF format, chain SA [auth D] mmCIF format, chain RB [auth G] mmCIF format, chain RA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain LC [auth I] mmCIF format, chain KC [auth I] mmCIF format, chain KB [auth F] mmCIF format, chain JC [auth I] mmCIF format, chain JB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain CD [auth L] mmCIF format, chain BD [auth L] mmCIF format, chain BC [auth H] mmCIF format, chain AC [auth H] mmCIF format, chain AB [auth E]	AB [auth E] AC [auth H] BC [auth H] BD [auth L] CD [auth L] AB [auth E], AC [auth H], BC [auth H], BD [auth L], CD [auth L], FA [auth C], GA [auth C], JB [auth F], JC [auth I], KB [auth F], KC [auth I], LC [auth I], P [auth A], Q [auth A], QB [auth G], R [auth A], RA [auth D], RB [auth G], SA [auth D], SB [auth G], SC [auth J], TC [auth J], XC [auth K], Y [auth B], YB [auth H], YC [auth K], Z [auth B], ZA [auth E], ZB [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain AC [auth H] Focus chain BC [auth H] Focus chain BD [auth L] Focus chain CD [auth L] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain JB [auth F] Focus chain JC [auth I] Focus chain KB [auth F] Focus chain KC [auth I] Focus chain LC [auth I] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QB [auth G] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RB [auth G] Focus chain SA [auth D] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain TC [auth J] Focus chain XC [auth K] Focus chain Y [auth B] Focus chain YB [auth H] Focus chain YC [auth K] Focus chain Z [auth B] Focus chain ZA [auth E] Focus chain ZB [auth H] Interactions & Density Focus chain AB [auth E] Focus chain AC [auth H] Focus chain BC [auth H] Focus chain BD [auth L] Focus chain CD [auth L] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain JB [auth F] Focus chain JC [auth I] Focus chain KB [auth F] Focus chain KC [auth I] Focus chain LC [auth I] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QB [auth G] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RB [auth G] Focus chain SA [auth D] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain TC [auth J] Focus chain XC [auth K] Focus chain Y [auth B] Focus chain YB [auth H] Focus chain YC [auth K] Focus chain Z [auth B] Focus chain ZA [auth E] Focus chain ZB [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.225 (DCC)
R-Value Work: 0.192 (Depositor), 0.194 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.91	α = 90
b = 183.272	β = 90
c = 183.183	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31530026
National Natural Science Foundation of China (NSFC)	China	31871005
National Natural Science Foundation of China (NSFC)	China	31770793
National Natural Science Foundation of China (NSFC)	China	31900981