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- PDB-5wtd: Structure of human serum transferrin bound ruthenium at N-lobe -

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Basic information

Entry
Database: PDB / ID: 5wtd
TitleStructure of human serum transferrin bound ruthenium at N-lobe
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / ruthenium transferrin N-lobe
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 / RUTHENIUM ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsSun, H. / Wang, M. / Lai, T.P. / Zhang, H. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grant Council705310P 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
DepositionDec 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)75,5434
Polymers75,2841
Non-polymers2593
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.113, 157.351, 107.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


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


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ru
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS NATURAL VARIANT.

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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: 3.84 Å3/Da / Density % sol: 67.94 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.6
Details: PIPES-Na 100 mM, disodium malonate 8 mM, PEG3350 17%, glycerol 18%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99182 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: 0.99182 Å / Relative weight: 1
ReflectionResolution: 2.501→50 Å / Num. obs: 51927 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 31.62 Å2 / Rmerge(I) obs: 0.056 / Net I/av σ(I): 35.494 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.501-2.5357.50.7910.828185.76
2.53-2.597.60.3960.968199.8
2.59-2.667.60.3280.9771100
2.66-2.737.60.2760.982199.9
2.73-2.817.70.2250.9881100
2.81-2.97.70.1790.9921100
2.9-37.70.1570.9921100
3-3.127.60.1270.9931100
3.12-3.267.60.090.9961100
3.26-3.447.60.0670.9971100
3.44-3.657.40.0490.999199.9
3.65-3.937.10.0380.999199.8
3.93-4.337.80.0280.999199.9
4.33-4.957.80.0240.999199.9
4.95-6.247.80.0230.999199.9
6.24-507.30.0190.999198

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1B

4x1b


Resolution: 2.501→37.187 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 22.5
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2141 3480 5.21 %
Rwork0.1802 --
obs0.1819 51927 86.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.37 Å2 / Biso mean: 48.7808 Å2 / Biso min: 18.15 Å2
Refinement stepCycle: final / Resolution: 2.501→37.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5015 0 9 155 5179
Biso mean--45.65 40.54 -
Num. residues----649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055151
X-RAY DIFFRACTIONf_angle_d0.7196964
X-RAY DIFFRACTIONf_chiral_restr0.043743
X-RAY DIFFRACTIONf_plane_restr0.004903
X-RAY DIFFRACTIONf_dihedral_angle_d8.7073085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.501-2.53530.2947880.25091589167754
2.5353-2.57150.221910.24481567165854
2.5715-2.60980.2365950.23221663175856
2.6098-2.65060.2161940.21331713180759
2.6506-2.69410.2614780.21181801187961
2.6941-2.74050.25381010.20961959206066
2.7405-2.79030.21611240.19662066219071
2.7903-2.8440.21311280.19482249237778
2.844-2.9020.24911480.20582570271886
2.902-2.96510.21991540.21542648280292
2.9651-3.0340.251640.21232823298796
3.034-3.10980.2681710.20722862303398
3.1098-3.19390.22631540.19782904305898
3.1939-3.28780.22641540.18352896305099
3.2878-3.39390.21261570.18492932308999
3.3939-3.51510.25881510.17712902305399
3.5151-3.65570.20031780.17232897307599
3.6557-3.82190.18311590.15912912307199
3.8219-4.02320.21971550.16082912306799
4.0232-4.27490.21151710.155329033074100
4.2749-4.60440.17981820.14632869305199
4.6044-5.06680.18491590.15032926308599
5.0668-5.79760.17841450.179729713116100
5.7976-7.29530.23181530.194129073060100
7.2953-37.1910.20581260.1832889301597
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)
12.01890.46180.31022.3910.8523.30420.00870.33030.0285-0.1728-0.0505-0.0544-0.18890.08380.03940.2610.06610.02590.3840.01080.079315.23110.4521-13.1863
21.31310.37720.52592.6160.15862.52790.1584-0.11850.1140.261-0.17560.2251-0.1705-0.17240.00080.3145-0.09770.07890.4338-0.06250.089413.91918.687518.6177
32.0920.57541.12342.33940.92253.3088-0.03110.14520.1836-0.2271-0.09720.142-0.24890.20950.0990.26230.04830.06220.29820.01050.117814.657516.7799-8.3191
43.95460.31310.26965.3419-0.63762.56560.4722-0.3126-0.1460.4472-0.4205-0.7689-0.33090.81420.00060.5287-0.3440.02140.76860.11280.31840.21134.7260.8584
53.370.7966-1.21592.3084-1.12253.57360.2962-0.04970.44440.6418-0.11170.5174-0.3775-0.1189-0.21390.6524-0.1930.09960.43870.03620.271935.023755.8624-14.6904
63.0570.61780.27342.8519-1.00531.76350.3607-0.38270.58670.9076-0.3748-0.019-0.5690.51120.00670.8101-0.3390.09140.70050.01550.310333.478441.43223.1003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 92 )A3 - 92
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 246 )A93 - 246
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 332 )A247 - 332
4X-RAY DIFFRACTION4chain 'A' and (resid 339 through 413 )A339 - 413
5X-RAY DIFFRACTION5chain 'A' and (resid 424 through 583 )A424 - 583
6X-RAY DIFFRACTION6chain 'A' and (resid 584 through 679 )A584 - 679

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