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- PDB-9vo7: Crystal structure of HuHF-C1, a HuHF varitant -

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Basic information

Entry
Database: PDB / ID: 9vo7
TitleCrystal structure of HuHF-C1, a HuHF varitant
ComponentsFerritin heavy chain, N-terminally processed
KeywordsMETAL BINDING PROTEIN / Ferritin
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: 2.6 Å
AuthorsWang, W.M. / Yao, H. / Gong, W.J. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,6812
Polymers20,6411
Non-polymers401
Water1,02757
1
A: Ferritin heavy chain, N-terminally processed
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)496,34648
Polymers495,38424
Non-polymers96224
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 area91550 Å2
ΔGint-456 kcal/mol
Surface area142400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.104, 179.104, 179.104
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-201-

CA

21A-323-

HOH

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Components

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


Mass: 20640.986 Da / Num. of mol.: 1 / Mutation: E28A/Y35A/E63A/H66A/K87Q/E108A/Y138A/Q142A
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
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: BL17U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 8078 / % possible obs: 100 % / Redundancy: 21.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.025 / Rrim(I) all: 0.117 / Χ2: 0.761 / Net I/σ(I): 7 / Num. measured all: 176897
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.6419.50.6323910.9760.9940.1440.6490.454100
2.64-2.6919.40.6293720.9750.9940.1440.6460.443100
2.69-2.7418.90.4884020.9840.9960.1130.5010.461100
2.74-2.819.30.4663830.9870.9970.1080.4790.485100
2.8-2.8620.80.3733910.9920.9980.0820.3820.489100
2.86-2.9321.20.3163970.9930.9980.0690.3230.501100
2.93-321.50.2723910.9950.9990.0590.2790.517100
3-3.0821.90.2353940.9960.9990.0510.2410.546100
3.08-3.1722.10.2013940.9960.9990.0430.2060.554100
3.17-3.2822.40.1763940.9970.9990.0380.180.567100
3.28-3.3922.20.1463980.9980.9990.0310.1490.61100
3.39-3.5321.50.1164000.99910.0250.1180.68100
3.53-3.6924.80.1024000.99910.0210.1040.746100
3.69-3.8825.30.0884000.9970.9990.0180.090.837100
3.88-4.1324.90.0744130.99910.0150.0750.881100
4.13-4.4524.30.0694010.99910.0140.0711.023100
4.45-4.8922.40.0614220.99910.0130.0621.088100
4.89-5.624.30.0614190.99910.0120.0620.986100
5.6-7.0522.80.0624330.99910.0130.0641.097100
7.05-5018.60.0484830.99910.0110.051.83599.8

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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: 2.6→41.09 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 807 10 %
Rwork0.2147 --
obs0.219 8071 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 1 57 1436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021413
X-RAY DIFFRACTIONf_angle_d0.4841907
X-RAY DIFFRACTIONf_dihedral_angle_d4.744187
X-RAY DIFFRACTIONf_chiral_restr0.032205
X-RAY DIFFRACTIONf_plane_restr0.002252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.33971300.25591168X-RAY DIFFRACTION100
2.76-2.970.32741300.25161173X-RAY DIFFRACTION100
2.97-3.270.28821310.24211177X-RAY DIFFRACTION100
3.27-3.740.2511330.20781205X-RAY DIFFRACTION100
3.75-4.710.19281370.17851222X-RAY DIFFRACTION100
4.72-41.090.25561460.21191319X-RAY DIFFRACTION100

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