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- PDB-6ipc: Non-native human ferritin 8-mer -

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Basic information

Entry
Database: PDB / ID: 6ipc
TitleNon-native human ferritin 8-mer
Components(Ferritin heavy chain) x 2
KeywordsOXIDOREDUCTASE / ferritin / 8-mer / inner disulfide bond
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.443 Å
AuthorsZang, J.C. / Chen, H. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaBX201700284 China
CitationJournal: Nat Commun / Year: 2019
Title: Disulfide-mediated conversion of 8-mer bowl-like protein architecture into three different nanocages.
Authors: Zang, J. / Chen, H. / Zhang, X. / Zhang, C. / Guo, J. / Du, M. / Zhao, G.
History
DepositionNov 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,02118
Polymers325,78516
Non-polymers2362
Water30617
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0109
Polymers162,8928
Non-polymers1181
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21060 Å2
ΔGint-66 kcal/mol
Surface area54690 Å2
MethodPISA
2
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0109
Polymers162,8928
Non-polymers1181
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21420 Å2
ΔGint-62 kcal/mol
Surface area54170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.304, 139.223, 139.114
Angle α, β, γ (deg.)90.10, 90.28, 90.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 20357.529 Da / Num. of mol.: 14 / Mutation: C90A, C102A, C130A, 140~145 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase
#2: Protein Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 20389.594 Da / Num. of mol.: 2 / Mutation: C90A, C102A, 140~145 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 0.1 M HEPES pH 7.5; 10% PEG 6000; 5% MPD

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 4.44→49.247 Å / Num. obs: 21483 / % possible obs: 87 % / Redundancy: 3.2 % / CC1/2: 1 / Net I/av σ(I): 4.7 / Net I/σ(I): 2.3
Reflection shellResolution: 4.443→4.602 Å / Rmerge(I) obs: 0.1971 / Num. unique obs: 495 / CC1/2: 1 / Rsym value: 0.275 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FHA

2fha


Resolution: 4.443→49.247 Å / SU ML: 0.6 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 39.76
RfactorNum. reflection% reflection
Rfree0.2766 883 4.17 %
Rwork0.2066 --
obs0.2098 21165 87.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.443→49.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20122 0 16 17 20155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520568
X-RAY DIFFRACTIONf_angle_d0.78927726
X-RAY DIFFRACTIONf_dihedral_angle_d15.76212374
X-RAY DIFFRACTIONf_chiral_restr0.0392898
X-RAY DIFFRACTIONf_plane_restr0.0043656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4434-4.72160.43461100.2562961X-RAY DIFFRACTION76
4.7216-5.08590.25112040.2353375X-RAY DIFFRACTION90
5.0859-5.5970.32151610.22873184X-RAY DIFFRACTION83
5.597-6.40540.38471290.23953795X-RAY DIFFRACTION97
6.4054-8.06440.30061160.21023669X-RAY DIFFRACTION95
8.0644-49.25020.21431630.16263298X-RAY DIFFRACTION85

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