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- PDB-9thr: Crystal structure of the human serum transferrin with Fe(III) bou... -

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Basic information

Entry
Database: PDB / ID: 9thr
TitleCrystal structure of the human serum transferrin with Fe(III) bound at the C-lobe only (treated with DMSO)
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / protein metalation / vanadium compounds
Function / homology
Function and homology information


iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / Post-translational protein phosphorylation / iron ion transport / clathrin-coated endocytic vesicle membrane / regulation of iron ion transport / ferrous iron binding / HFE-transferrin receptor complex / Iron uptake and transport / recycling endosome / regulation of protein stability / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / antibacterial humoral response / Platelet degranulation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / intracellular iron ion homeostasis / transmembrane transporter binding / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
BICARBONATE ION / : / MALONIC ACID / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPaolillo, M. / Ferraro, G. / Banneville, A.S. / Cornaciu, I. / Pica, A. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Commun Chem / Year: 2026
Title: First crystal structure of an adduct formed upon reaction of a vanadium compound with human serum transferrin.
Authors: Banneville, A.S. / Lucignano, R. / Paolillo, M. / Cuomo, V. / Chino, M. / Ferraro, G. / Picone, D. / Garribba, E. / Cornaciu-Hoffmann, I. / Pica, A. / Merlino, A.
History
DepositionDec 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8429
Polymers75,2841
Non-polymers5578
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.098, 156.774, 107.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 75284.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02787

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Non-polymers , 5 types, 47 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.82 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 3350, 16% (v/v) glycerol, 8 mM disodium malonate, 150 mM Na-PIPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.2→74.32 Å / Num. obs: 18284 / % possible obs: 93.7 % / Redundancy: 10.6 % / CC1/2: 0.995 / Net I/σ(I): 12.4
Reflection shellResolution: 3.2→3.25 Å / Num. unique obs: 914 / CC1/2: 0.921

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→74.32 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.801 / SU B: 17.373 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / ESU R Free: 0.455
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2491 914 5.019 %
Rwork0.1797 17295 -
all0.183 --
obs-18209 93.75 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.185 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 3.2→74.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 34 39 5211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135316
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154895
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6437186
X-RAY DIFFRACTIONr_angle_other_deg1.2471.58811335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1325663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2823.045266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57915901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5851526
X-RAY DIFFRACTIONr_chiral_restr0.0670.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021196
X-RAY DIFFRACTIONr_nbd_refined0.2150.21187
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24823
X-RAY DIFFRACTIONr_nbtor_refined0.170.22493
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.27
X-RAY DIFFRACTIONr_nbd_other0.1420.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0410.25
X-RAY DIFFRACTIONr_mcbond_it3.1724.5492655
X-RAY DIFFRACTIONr_mcbond_other3.1724.5492654
X-RAY DIFFRACTIONr_mcangle_it5.1996.823317
X-RAY DIFFRACTIONr_mcangle_other5.1996.8213318
X-RAY DIFFRACTIONr_scbond_it3.1994.8872660
X-RAY DIFFRACTIONr_scbond_other3.1984.8872646
X-RAY DIFFRACTIONr_scangle_it5.3237.1883869
X-RAY DIFFRACTIONr_scangle_other5.3257.1883855
X-RAY DIFFRACTIONr_lrange_it7.99452.9435782
X-RAY DIFFRACTIONr_lrange_other7.99452.9445783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2830.286630.2241166X-RAY DIFFRACTION87.1631
3.283-3.3730.292660.2331232X-RAY DIFFRACTION94.1945
3.373-3.470.325450.227842X-RAY DIFFRACTION65.6551
3.47-3.5770.268650.2051235X-RAY DIFFRACTION100
3.577-3.6940.29450.202875X-RAY DIFFRACTION73.8363
3.694-3.8230.29630.1981176X-RAY DIFFRACTION100
3.823-3.9670.238520.188974X-RAY DIFFRACTION86.9492
3.967-4.1290.176570.1581086X-RAY DIFFRACTION100
4.129-4.3120.19540.1361031X-RAY DIFFRACTION100
4.312-4.5210.178540.1341009X-RAY DIFFRACTION100
4.521-4.7650.203490.137938X-RAY DIFFRACTION100
4.765-5.0530.196480.133902X-RAY DIFFRACTION100
5.053-5.40.281440.175849X-RAY DIFFRACTION100
5.4-5.830.253420.187801X-RAY DIFFRACTION100
5.83-6.3820.311390.199728X-RAY DIFFRACTION100
6.382-7.1290.315360.183679X-RAY DIFFRACTION100
7.129-8.2190.198300.144599X-RAY DIFFRACTION99.8413
8.219-10.0360.191260.163511X-RAY DIFFRACTION100
10.036-14.0650.186220.217407X-RAY DIFFRACTION100
14.065-74.320.722140.319250X-RAY DIFFRACTION97.7778

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