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- PDB-9von: Crystal strucrue of HuHF-71-Cur complex -

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Basic information

Entry
Database: PDB / ID: 9von
TitleCrystal strucrue of HuHF-71-Cur 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
curcumin / : / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,88418
Polymers157,8268
Non-polymers3,05910
Water8,467470
1
A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,65354
Polymers473,47724
Non-polymers9,17630
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area88850 Å2
ΔGint-310 kcal/mol
Surface area140130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.210, 181.210, 181.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11B-337-

HOH

21B-343-

HOH

31H-304-

HOH

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Components

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


Mass: 19728.197 Da / Num. of mol.: 8
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-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.: 8 / Source method: obtained synthetically / Formula: C21H20O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
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: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→48.43 Å / Num. obs: 68568 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.418 / Rpim(I) all: 0.094 / Rrim(I) all: 0.428 / Net I/σ(I): 8.2 / Num. measured all: 1407429
Reflection shellResolution: 2.5→2.56 Å / % possible obs: 100 % / Redundancy: 20.8 % / Rmerge(I) obs: 3.237 / Num. measured all: 95747 / Num. unique obs: 4595 / CC1/2: 0.484 / Rpim(I) all: 0.725 / Rrim(I) all: 3.318 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.43 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 3340 4.88 %
Rwork0.1981 --
obs0.2 68411 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 218 470 11552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811272
X-RAY DIFFRACTIONf_angle_d1.23315200
X-RAY DIFFRACTIONf_dihedral_angle_d12.7161544
X-RAY DIFFRACTIONf_chiral_restr0.051632
X-RAY DIFFRACTIONf_plane_restr0.0172024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.3441720.27142665X-RAY DIFFRACTION100
2.54-2.570.35631270.26522702X-RAY DIFFRACTION100
2.57-2.610.28481240.27642747X-RAY DIFFRACTION100
2.61-2.660.34531230.25852671X-RAY DIFFRACTION100
2.66-2.70.31581390.26622727X-RAY DIFFRACTION100
2.7-2.750.35121480.26252672X-RAY DIFFRACTION100
2.75-2.80.30771260.25912675X-RAY DIFFRACTION100
2.8-2.860.3065990.23632779X-RAY DIFFRACTION100
2.86-2.920.28851250.2362708X-RAY DIFFRACTION100
2.93-2.990.27441280.22622674X-RAY DIFFRACTION100
2.99-3.070.28381400.23222721X-RAY DIFFRACTION100
3.07-3.150.27081470.2222667X-RAY DIFFRACTION100
3.15-3.240.30721510.22872727X-RAY DIFFRACTION100
3.24-3.350.27131340.20762697X-RAY DIFFRACTION100
3.35-3.470.22151340.18072697X-RAY DIFFRACTION100
3.47-3.610.21151390.17132730X-RAY DIFFRACTION100
3.61-3.770.17791550.16862690X-RAY DIFFRACTION100
3.77-3.970.18891380.16272710X-RAY DIFFRACTION100
3.97-4.220.18721600.15172716X-RAY DIFFRACTION100
4.22-4.540.17971400.15012729X-RAY DIFFRACTION100
4.54-50.19581300.1572735X-RAY DIFFRACTION100
5-5.720.19391540.18822746X-RAY DIFFRACTION100
5.72-7.20.25631600.2142749X-RAY DIFFRACTION100
7.21-48.430.20551470.18852737X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 18.513 Å / Origin y: 120.624 Å / Origin z: 56.7952 Å
111213212223313233
T0.2735 Å2-0.0186 Å20.0245 Å2-0.2881 Å20.0145 Å2--0.3156 Å2
L0.2034 °2-0.005 °20.0085 °2-0.1988 °2-0.0197 °2--0.217 °2
S-0.0004 Å °-0.0426 Å °-0.0656 Å °0.0412 Å °0.0118 Å °0.1049 Å °0.0423 Å °-0.0897 Å °-0.013 Å °
Refinement TLS groupSelection details: all

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