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- PDB-9vom: Crystal strucrue of HuHF-C2-AZB complex -

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Basic information

Entry
Database: PDB / ID: 9vom
TitleCrystal strucrue of HuHF-C2-AZB complex
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
: / : / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)20,5666
Polymers20,0671
Non-polymers4995
Water3,783210
1
A: Ferritin heavy chain, N-terminally processed
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)493,592144
Polymers481,61724
Non-polymers11,974120
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 area98840 Å2
ΔGint-1179 kcal/mol
Surface area135450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.456, 183.456, 183.456
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-203-

MG

21A-204-

MG

31A-305-

HOH

41A-399-

HOH

51A-495-

HOH

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Components

#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
#2: Chemical ChemComp-A1ES0 / 3-[(E)-phenyldiazenyl]aniline


Mass: 197.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11N3 / 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-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
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: 61.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Bicine MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18428 / % possible obs: 100 % / Redundancy: 25.2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.019 / Rrim(I) all: 0.097 / Χ2: 0.735 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2-2.0326.20.5628900.9650.9910.1110.5730.449
2.03-2.0726.50.4768980.980.9950.0940.4850.455
2.07-2.1126.20.428900.9840.9960.0830.4280.474
2.11-2.15260.3499060.9880.9970.0690.3560.485
2.15-2.225.70.3029070.9890.9970.060.3080.506
2.2-2.2525.10.2818960.990.9970.0570.2860.538
2.25-2.3123.30.2598920.9910.9980.0550.2640.607
2.31-2.3725.90.2318940.9940.9990.0460.2350.637
2.37-2.4426.30.219280.9940.9980.0410.2140.611
2.44-2.5226.50.1778910.9960.9990.0350.180.642
2.52-2.6125.70.1639180.9960.9990.0320.1660.676
2.61-2.7125.20.1439060.9970.9990.0290.1460.724
2.71-2.8423.30.1249180.9970.9990.0260.1270.817
2.84-2.99260.1099200.9970.9990.0220.1110.947
2.99-3.1725.90.0969280.9980.9990.0190.0981.028
3.17-3.4225.50.0849290.99810.0170.0851.147
3.42-3.7623.60.0689300.99910.0140.071.244
3.76-4.3125.80.0599460.99910.0120.061.182
4.31-5.4323.60.0549730.99910.0110.0550.98
5.43-5022.10.0411068110.0090.0420.54

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.31 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 1840 10 %
Rwork0.174 --
obs0.1764 18407 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 33 210 1580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071392
X-RAY DIFFRACTIONf_angle_d0.7181878
X-RAY DIFFRACTIONf_dihedral_angle_d4.675184
X-RAY DIFFRACTIONf_chiral_restr0.041204
X-RAY DIFFRACTIONf_plane_restr0.006247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.21841390.16071249X-RAY DIFFRACTION100
2.06-2.120.20621370.15631239X-RAY DIFFRACTION100
2.12-2.180.1791380.14681246X-RAY DIFFRACTION100
2.18-2.260.18351390.1491241X-RAY DIFFRACTION100
2.26-2.350.20351390.16431248X-RAY DIFFRACTION100
2.35-2.460.22521380.17441249X-RAY DIFFRACTION100
2.46-2.590.20391390.18151251X-RAY DIFFRACTION100
2.59-2.750.2211410.18191267X-RAY DIFFRACTION100
2.75-2.960.21891410.18561271X-RAY DIFFRACTION100
2.97-3.260.18141420.17891275X-RAY DIFFRACTION100
3.26-3.730.18411430.16041293X-RAY DIFFRACTION100
3.74-4.70.16941480.15071321X-RAY DIFFRACTION100
4.71-35.310.22771560.21281417X-RAY DIFFRACTION99

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