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- PDB-5x5p: Human serum transferrin bound to ruthenium NTA -

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Basic information

Entry
Database: PDB / ID: 5x5p
TitleHuman serum transferrin bound to ruthenium NTA
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / transferrin / ruthenium / NTA
Function / homology
Function and homology information


iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin ...Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / MALONATE ION / NITRILOTRIACETIC ACID / RUTHENIUM ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSun, H. / Wang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grants Council, HKSAR GOV.705310P Hong Kong
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: Binding of ruthenium and osmium at non‐iron sites of transferrin accounts for their iron-independent cellular uptake.
Authors: Wang, M. / Wang, H. / Xu, X. / Lai, T.P. / Zhou, Y. / Hao, Q. / Li, H. / Sun, H.
History
DepositionFeb 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,26610
Polymers75,2991
Non-polymers9679
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-24 kcal/mol
Surface area28190 Å2
Unit cell
Length a, b, c (Å)136.748, 158.395, 106.610
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 A

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


Mass: 75298.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Human serum transferrin from Sigma. (Cat.No. T2036)
Source: (natural) Homo sapiens (human) / References: UniProt: P02787

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Non-polymers , 6 types, 18 molecules

#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ru
#5: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO6
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 3.83 Å3/Da / Density % sol: 67.9 % / Description: Half-moon like
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PIPES-Na 100mM pH 6.6, disodium malonate 8mM, PEG 3350 18%, glycerol 17%

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen flow
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.14026 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2014
RadiationMonochromator: Graphite filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14026 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 32206 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.044 / Rrim(I) all: 0.133 / Χ2: 0.974 / Net I/σ(I): 7 / Num. measured all: 298701
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.758.80.63615930.9050.2260.6760.939100
2.75-2.88.40.55115800.940.2010.5870.933100
2.8-2.858.70.47315910.9510.1690.5030.939100
2.85-2.919.20.41615970.9650.1440.4410.945100
2.91-2.979.70.36515890.9750.1230.3860.931100
2.97-3.049.70.3215920.9710.1080.3380.951100
3.04-3.129.70.28915840.9760.0980.3050.981100
3.12-3.29.60.23215850.9720.080.2460.971100
3.2-3.39.60.19116100.9850.0660.2020.959100
3.3-3.49.60.16716130.9850.0570.1770.976100
3.4-3.529.30.15415700.9890.0540.1630.98799.9
3.52-3.668.60.1316080.980.0480.1390.944100
3.66-3.8390.1216120.9880.0430.1280.969100
3.83-4.039.90.11316210.990.0390.120.973100
4.03-4.299.80.10416090.9910.0360.110.954100
4.29-4.629.70.09815980.990.0340.1040.922100
4.62-5.089.30.09416230.990.0330.10.878100
5.08-5.818.60.09316450.9910.0340.0990.844100
5.81-7.329.70.09316480.9910.0310.0980.887100
7.32-508.80.11717380.9840.0410.1241.581100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QYT

3qyt


Resolution: 2.7→49.255 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2225 / WRfactor Rwork: 0.1738 / FOM work R set: 0.8594 / SU B: 16.783 / SU ML: 0.158 / SU R Cruickshank DPI: 0.2348 / SU Rfree: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1628 5.1 %RANDOM
Rwork0.1682 ---
obs0.1708 32206 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.47 Å2 / Biso mean: 48.231 Å2 / Biso min: 8.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0 Å20 Å2
2---2.69 Å2-0 Å2
3---3.75 Å2
Refinement stepCycle: final / Resolution: 2.7→49.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 39 9 5017
Biso mean--59.99 34.27 -
Num. residues----649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195125
X-RAY DIFFRACTIONr_bond_other_d0.0020.024595
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9636939
X-RAY DIFFRACTIONr_angle_other_deg0.933310702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30724.529223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9815842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5641523
X-RAY DIFFRACTIONr_chiral_restr0.0630.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021022
X-RAY DIFFRACTIONr_rigid_bond_restr6.24535087
X-RAY DIFFRACTIONr_sphericity_bonded44.87954961
LS refinement shellResolution: 2.697→2.767 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 111 -
Rwork0.244 2158 -
all-2269 -
obs--96.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76450.03130.16130.02020.00090.036-0.0425-0.0040.0107-0.0150.0319-0.0127-0.0053-0.00480.01060.1191-0.00660.0090.12170.00160.015515.585410.3086-13.1904
20.3044-0.1580.17371.1666-0.15460.10370.0029-0.0090.00680.0011-0.00220.04180.0111-0.0047-0.00060.0981-0.00180.00640.1124-0.00270.002513.912218.930318.4814
30.321-0.19650.11760.1221-0.07140.0437-0.00390.03290.00260.0006-0.0019-0.0031-0.00330.01840.00580.0981-0.0102-0.00560.1362-0.00720.01414.656216.6504-8.6703
40.7092-0.53680.0411.6735-0.45161.7460.1285-0.063-0.13810.0316-0.094-0.1257-0.070.1392-0.03440.123-0.065-0.02540.12680.02330.080339.564635.21850.7668
51.32210.4156-0.15650.8925-0.10710.02420.07410.00840.05290.0859-0.06080.0855-0.0039-0.0025-0.01330.104-0.0135-0.00210.12150.00410.010235.010156.2105-15.2237
60.03610.064-01.2078-0.52131.31390.0333-0.06310.01440.1925-0.05550.0012-0.22150.09460.02220.1131-0.04230.02710.1391-0.01540.014132.883541.68792.7915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 92
2X-RAY DIFFRACTION2A93 - 246
3X-RAY DIFFRACTION3A247 - 331
4X-RAY DIFFRACTION4A339 - 425
5X-RAY DIFFRACTION5A426 - 577
6X-RAY DIFFRACTION6A581 - 679

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