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- PDB-9h4v: Crystal structure of the adduct formed upon reaction of aurothiom... -

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Basic information

Entry
Database: PDB / ID: 9h4v
TitleCrystal structure of the adduct formed upon reaction of aurothiomalate with human serum transferrin (apo-form)
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Myochrysine / metallodrug / gold-based drugs / protein metalation / human transferrin / aurothiomalate
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 / basal plasma membrane / osteoclast differentiation / Iron uptake and transport ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / Iron uptake and transport / cellular response to iron ion / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / ferrous iron binding / iron ion transport / regulation of iron ion transport / HFE-transferrin receptor complex / 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) / Cargo recognition for clathrin-mediated endocytosis / antibacterial humoral response / Clathrin-mediated endocytosis / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / cytoplasmic vesicle / blood microparticle / vesicle / secretory granule lumen / transmembrane transporter binding / intracellular iron ion homeostasis / 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
: / CITRIC ACID / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsTroisi, R. / Galardo, F. / Messori, L. / Sica, F. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca2022JMFC3X Italy
CitationJournal: Inorg Chem Front / Year: 2025
Title: The X-ray structure of the adduct formed upon reaction of aurothiomalate with apo-transferrin: gold binding sites and a unique transferrin structure along the apo/holo transition pathway
Authors: Troisi, R. / Galardo, F. / Messori, L. / Sica, F. / Merlino, A.
History
DepositionOct 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serotransferrin
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,07030
Polymers150,5692
Non-polymers5,50128
Water1448
1
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,82614
Polymers75,2841
Non-polymers2,54113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,24416
Polymers75,2841
Non-polymers2,95915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.472, 99.714, 198.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 75284.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02787
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG 3350 and 200 mM trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 3.02→89.25 Å / Num. obs: 33617 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 1 / Net I/σ(I): 7.8
Reflection shellResolution: 3.02→3.07 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1641 / CC1/2: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→89.25 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.898 / SU B: 30.025 / SU ML: 0.488 / Cross valid method: THROUGHOUT / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 1595 4.8 %RANDOM
Rwork0.24325 ---
obs0.24578 31963 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.632 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å2-0 Å2
2---0.25 Å20 Å2
3---5.43 Å2
Refinement stepCycle: 1 / Resolution: 3.02→89.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10488 0 137 8 10633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01210893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.961.83614761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05651352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.976552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.399101833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028377
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6448.3665408
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.03215.0526757
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4548.5295485
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.53895.3416257
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.021→3.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 108 -
Rwork0.38 2282 -
obs--97.71 %

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