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- PDB-28mr: X-ray structure of the adduct between human serum transferrin wit... -

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Basic information

Entry
Database: PDB / ID: 28mr
TitleX-ray structure of the adduct between human serum transferrin with Fe3+ bound at the C-lobe and diruthenium tetraacetate chloride
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / human transferrin / diruthenium / iron / drug delivery / protein-metal interaction
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 / Post-translational protein phosphorylation ...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 / Post-translational protein phosphorylation / iron ion transport / clathrin-coated endocytic vesicle membrane / regulation of protein stability / HFE-transferrin receptor complex / cellular response to iron ion / ferrous iron binding / Iron uptake and transport / positive regulation of receptor-mediated endocytosis / recycling endosome / 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 / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Clathrin-mediated endocytosis / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / intracellular iron ion homeostasis / transmembrane transporter binding / early endosome / cell surface receptor signaling pathway / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / enzyme binding / cell surface / : / 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
ACETATE ION / : / MALONATE ION / RUTHENIUM ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.262 Å
AuthorsFerraro, G. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)2022JMFC3X Italy
CitationJournal: Dalton Trans / Year: 2026
Title: Ru and Rh binding sites in the structure of human serum transferrin with Fe 3+ bound at the C-lobe.
Authors: Banneville, A.S. / Ferraro, G. / D'Elia, R. / Cornaciu-Hoffmann, I. / Pica, A. / Merlino, A.
History
DepositionFeb 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7307
Polymers75,2841
Non-polymers4466
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.936, 156.712, 107.145
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1142-

HOH

21A-1156-

HOH

31A-1164-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 , 7 types, 389 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ru / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 67.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
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: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.262→103.116 Å / Num. obs: 30700 / % possible obs: 93.9 % / Redundancy: 12.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.208 / Net I/σ(I): 9.8
Reflection shellResolution: 2.262→2.502 Å / Num. unique obs: 1535 / CC1/2: 0.734

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.262→103.116 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.04 / SU ML: 0.168 / Cross valid method: FREE R-VALUE / ESU R: 0.462 / ESU R Free: 0.287
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2344 1528 4.977 %
Rwork0.1791 29172 -
all0.182 --
obs-30700 56.823 %
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: 44.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.458 Å20 Å2-0 Å2
2---0.335 Å20 Å2
3---0.793 Å2
Refinement stepCycle: LAST / Resolution: 2.262→103.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 20 383 5604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125407
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164976
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.8327320
X-RAY DIFFRACTIONr_angle_other_deg0.5281.77811534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5695679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.091527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68110921
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.80210246
X-RAY DIFFRACTIONr_chiral_restr0.0690.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021213
X-RAY DIFFRACTIONr_nbd_refined0.2220.21277
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.24900
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22627
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2311
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.29
X-RAY DIFFRACTIONr_nbd_other0.1320.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.211
X-RAY DIFFRACTIONr_mcbond_it3.7644.5482708
X-RAY DIFFRACTIONr_mcbond_other3.7614.5482707
X-RAY DIFFRACTIONr_mcangle_it6.1098.1563389
X-RAY DIFFRACTIONr_mcangle_other6.1088.1573390
X-RAY DIFFRACTIONr_scbond_it4.2865.0392699
X-RAY DIFFRACTIONr_scbond_other4.2855.0392700
X-RAY DIFFRACTIONr_scangle_it7.2079.0733931
X-RAY DIFFRACTIONr_scangle_other7.2069.0733932
X-RAY DIFFRACTIONr_lrange_it10.18641.8816243
X-RAY DIFFRACTIONr_lrange_other10.16641.9996154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.262-2.3210.166100.2171410.21339330.9870.9723.83930.22
2.321-2.3840.26200.2893840.28738500.9510.93910.49350.29
2.384-2.4530.432250.2975030.30337470.8980.94314.09130.296
2.453-2.5290.265270.2596730.2636580.950.95919.13610.255
2.529-2.6120.329420.2678920.2735270.9370.95626.48140.256
2.612-2.7030.253530.25710720.25734080.9590.96233.01060.243
2.703-2.8050.333690.24914740.25333240.9290.96346.420.229
2.805-2.920.311980.22818000.23231730.9480.96959.81720.202
2.92-3.050.273990.20920780.21230760.9570.97170.77370.186
3.05-3.1980.291190.19622280.20129040.9440.97480.81960.172
3.198-3.3710.2581320.19323330.19727910.9530.97688.31960.172
3.371-3.5750.2521390.19223700.19626580.9540.97794.39430.175
3.575-3.8220.2361320.18423150.18724890.9730.98198.31260.173
3.822-4.1280.1881090.15822150.1623240.9770.9871000.151
4.128-4.5210.1961150.1320360.13421510.9750.9911000.129
4.521-5.0530.15910.12518440.12619350.9870.9911000.121
5.053-5.8330.205890.15816460.1617360.9790.98799.94240.158
5.833-7.1380.235700.1714070.17314830.9610.98399.59540.169
7.138-10.070.176550.15511050.15611630.9840.98599.74210.175
10.07-103.1160.443340.2696560.2766970.8140.94798.99570.326

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