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- PDB-21le: Crystal strucrue of HuHF-C2-CAR complex -

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Basic information

Entry
Database: PDB / ID: 21le
TitleCrystal strucrue of HuHF-C2-CAR 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3705
Polymers20,0671
Non-polymers3034
Water4,270237
1
A: Ferritin heavy chain, N-terminally processed
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)488,883120
Polymers481,61724
Non-polymers7,26696
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 area93410 Å2
ΔGint-980 kcal/mol
Surface area138760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.708, 182.708, 182.708
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-

MG

21A-202-

MG

31A-308-

HOH

41A-411-

HOH

51A-473-

HOH

61A-485-

HOH

71A-530-

HOH

81A-531-

HOH

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Components

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


Mass: 20067.391 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-I4E / CARMUSTINE / 1,3-bis(2-chloroethyl)-1-nitroso-urea


Mass: 214.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9Cl2N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
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: 0.9785 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: 18180 / % possible obs: 100 % / Redundancy: 36.5 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.032 / Rrim(I) all: 0.188 / Χ2: 2.638 / Net I/σ(I): 6.2 / Num. measured all: 663957
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.0339.60.3058840.9880.9970.0490.3091.446100
2.03-2.0739.60.298890.990.9970.0470.2941.572100
2.07-2.1139.20.2798810.9920.9980.0450.2831.69100
2.11-2.1538.40.2618860.9910.9980.0430.2641.829100
2.15-2.237.90.2498810.9940.9980.0410.2531.952100
2.2-2.2536.60.2448820.9920.9980.0410.2482.026100
2.25-2.31380.2399000.9930.9980.0390.2432.102100
2.31-2.37370.2298810.9930.9980.0380.2322.257100
2.37-2.4438.90.2288970.9950.9990.0370.2312.322100
2.44-2.5238.40.2168910.9940.9980.0360.2192.55100
2.52-2.6137.60.2129050.9940.9980.0350.2152.515100
2.61-2.7135.70.2018910.9950.9990.0340.2042.61299.9
2.71-2.8436.90.1958980.9960.9990.0330.1982.856100
2.84-2.9935.90.1839070.9940.9990.0310.1863.152100
2.99-3.1736.80.1759120.9950.9990.0290.1783.248100
3.17-3.4235.50.1669250.9950.9990.0290.1693.461100
3.42-3.7633.90.1569220.9960.9990.0280.1583.816100
3.76-4.3134.30.1529490.9970.9990.0270.1544.031100
4.31-5.4332.50.159470.9960.9990.0270.1524.022100
5.43-5029.50.1510520.9950.9990.0280.1533.82699.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.45 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 1816 10 %
Rwork0.1496 --
obs0.1534 18156 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→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 15 237 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121371
X-RAY DIFFRACTIONf_angle_d0.9811850
X-RAY DIFFRACTIONf_dihedral_angle_d5.518188
X-RAY DIFFRACTIONf_chiral_restr0.052204
X-RAY DIFFRACTIONf_plane_restr0.008244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.19151370.14081231X-RAY DIFFRACTION100
2.06-2.120.20271360.13291230X-RAY DIFFRACTION100
2.12-2.190.16631350.12111215X-RAY DIFFRACTION100
2.19-2.260.16931390.12761245X-RAY DIFFRACTION100
2.26-2.350.18621350.14091224X-RAY DIFFRACTION100
2.35-2.460.18191370.14731222X-RAY DIFFRACTION100
2.46-2.590.18371380.15441240X-RAY DIFFRACTION100
2.59-2.750.19771390.15211251X-RAY DIFFRACTION100
2.75-2.970.17981380.15051248X-RAY DIFFRACTION100
2.97-3.260.22061400.15761259X-RAY DIFFRACTION100
3.27-3.730.16871420.13721278X-RAY DIFFRACTION100
3.74-4.70.17681440.14341299X-RAY DIFFRACTION100
4.7-30.450.2031560.19451398X-RAY DIFFRACTION99

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