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- PDB-21kv: Crystal strucrue of HuHF-C2-DAC complex -

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Basic information

Entry
Database: PDB / ID: 21kv
TitleCrystal strucrue of HuHF-C2-DAC complex
ComponentsFerritin heavy chain, N-terminally processed
KeywordsMETAL BINDING PROTEIN / HuHF / Dacarbazine / Complex / Protein design
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. / Gong, W.J. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22577068 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
DepositionDec 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6529
Polymers40,1352
Non-polymers5177
Water8,233457
1
A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)487,827108
Polymers481,61724
Non-polymers6,20984
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_544x,-y-1/2,-z-1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation27_554-x+1/2,y,-z-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation38_545-x+1/2,-y-1/2,z1
crystal symmetry operation41_545z+1/2,x-1/2,y1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
Buried area94250 Å2
ΔGint-834 kcal/mol
Surface area143470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.663, 184.663, 184.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-204-

MG

21B-203-

MG

31A-373-

HOH

41A-520-

HOH

51B-382-

HOH

61B-529-

HOH

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Components

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


Mass: 20067.391 Da / Num. of mol.: 2
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-A1E2W / 4-(dimethylaminodiazenyl)-1H-imidazole-5-carboxamide


Mass: 182.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 291 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: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35253 / % possible obs: 100 % / Redundancy: 19.28 % / CC1/2: 0.9971 / Rmerge(I) obs: 0.1513 / Rpim(I) all: 0.0355 / Rrim(I) all: 0.1555 / Net I/σ(I): 24.73
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.5995 / Mean I/σ(I) obs: 7.21 / Num. unique obs: 2569 / CC1/2: 0.9353 / Rpim(I) all: 0.1431 / Rrim(I) all: 0.6166

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.29 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 1993 5.66 %
Rwork0.1681 --
obs0.1701 35215 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 31 457 3162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192746
X-RAY DIFFRACTIONf_angle_d1.1783710
X-RAY DIFFRACTIONf_dihedral_angle_d6.998374
X-RAY DIFFRACTIONf_chiral_restr0.074408
X-RAY DIFFRACTIONf_plane_restr0.011490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.22461410.1872277X-RAY DIFFRACTION96
2.05-2.10.33271480.24142340X-RAY DIFFRACTION100
2.1-2.160.1871400.17682342X-RAY DIFFRACTION100
2.16-2.230.23721370.16722368X-RAY DIFFRACTION100
2.23-2.310.31341430.24172370X-RAY DIFFRACTION99
2.31-2.410.20841390.15962366X-RAY DIFFRACTION100
2.41-2.520.17731450.16332386X-RAY DIFFRACTION100
2.52-2.650.19581390.16792366X-RAY DIFFRACTION100
2.65-2.810.22061430.17122370X-RAY DIFFRACTION100
2.82-3.030.18351430.14892380X-RAY DIFFRACTION100
3.03-3.340.18451410.15462381X-RAY DIFFRACTION100
3.34-3.820.16391420.14892408X-RAY DIFFRACTION100
3.82-4.810.17391420.14562421X-RAY DIFFRACTION100
4.82-41.290.19221500.17892447X-RAY DIFFRACTION100

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