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- PDB-9vod: Crystal strucrue of HuHF-C2-Cur complex 1 -

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Basic information

Entry
Database: PDB / ID: 9vod
TitleCrystal strucrue of HuHF-C2-Cur complex 1
ComponentsFerritin heavy chain, N-terminally processed
KeywordsMETAL BINDING PROTEIN / Ferritin variant
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / Iron uptake and transport / 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 / cytoplasm / cytosol
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
curcumin / : / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsWang, W.M. / Yao, H. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118 China
CitationJournal: Small / Year: 2026
Title: Redesign of the Ferritin Ferroxidase Center for Universal Molecular Binding or Specific Recognition.
Authors: Wang, W. / Yao, H. / Gong, W. / Ma, D. / Qiao, J. / Zhang, Y. / Wu, L. / Fan, C. / Zhao, Y. / Wang, Z. / Jia, Z. / Guo, Y. / Zhang, N. / Zhao, G. / Yun, Y. / Wang, H.
History
DepositionJul 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5806
Polymers20,0671
Non-polymers5135
Water4,846269
1
A: Ferritin heavy chain, N-terminally processed
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)493,927144
Polymers481,61724
Non-polymers12,310120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area98020 Å2
ΔGint-1155 kcal/mol
Surface area134810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.538, 183.538, 183.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-202-

MG

21A-203-

MG

31A-204-

CA

41A-311-

HOH

51A-428-

HOH

61A-501-

HOH

71A-555-

HOH

81A-569-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin heavy chain, N-terminally processed


Mass: 20067.391 Da / Num. of mol.: 1
Mutation: E28A/Y35A/Y55A/H58A/Q59A/E62A/E63A/H66A/K69A/K87Q/E108A/H137A/Y138A/E141A/Q142A/K144A/E148A
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

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-CC9 / curcumin / (1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,6-diene-3,5-dione


Mass: 368.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Bincine MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→19.57 Å / Num. obs: 20691 / % possible obs: 99.63 % / Redundancy: 35.2 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.062 / Net I/σ(I): 16.8
Reflection shellResolution: 1.92→1.99 Å / Mean I/σ(I) obs: 10.14 / Num. unique obs: 1958 / CC1/2: 0.99 / Rrim(I) all: 0.223

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→19.57 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 3701 9.75 %
Rwork0.1533 --
obs0.1572 20691 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 31 269 1637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071404
X-RAY DIFFRACTIONf_angle_d0.8271898
X-RAY DIFFRACTIONf_dihedral_angle_d11.509194
X-RAY DIFFRACTIONf_chiral_restr0.049206
X-RAY DIFFRACTIONf_plane_restr0.006253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.44811260.34361174X-RAY DIFFRACTION88
1.95-1.970.24531400.20441349X-RAY DIFFRACTION100
1.97-20.2361430.16451312X-RAY DIFFRACTION100
2-2.030.17131420.15181323X-RAY DIFFRACTION100
2.03-2.060.19051470.14621323X-RAY DIFFRACTION100
2.06-2.10.1931390.14351306X-RAY DIFFRACTION100
2.1-2.130.22251400.14741351X-RAY DIFFRACTION100
2.13-2.170.1921330.14171289X-RAY DIFFRACTION100
2.17-2.210.17351490.13741337X-RAY DIFFRACTION100
2.21-2.260.16341390.14161321X-RAY DIFFRACTION100
2.26-2.310.19751390.14251333X-RAY DIFFRACTION100
2.31-2.360.19411490.15961330X-RAY DIFFRACTION100
2.36-2.420.18781410.15681305X-RAY DIFFRACTION100
2.42-2.480.2051420.15351320X-RAY DIFFRACTION100
2.48-2.560.2151480.15791312X-RAY DIFFRACTION100
2.56-2.640.18071470.15661347X-RAY DIFFRACTION100
2.64-2.730.20271390.16161297X-RAY DIFFRACTION100
2.73-2.840.20721510.16331323X-RAY DIFFRACTION100
2.84-2.970.1751460.14721311X-RAY DIFFRACTION100
2.97-3.130.21111450.1561334X-RAY DIFFRACTION100
3.13-3.320.17751420.14641328X-RAY DIFFRACTION100
3.32-3.580.18261420.13931316X-RAY DIFFRACTION100
3.58-3.930.17341430.13481330X-RAY DIFFRACTION100
3.94-4.50.14581400.13561325X-RAY DIFFRACTION100
4.5-5.640.17011480.15591324X-RAY DIFFRACTION100
5.65-19.570.23541410.1781338X-RAY DIFFRACTION100

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