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- PDB-7ffu: Osmium-bound human serum transferrin -

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Basic information

Entry
Database: PDB / ID: 7ffu
TitleOsmium-bound human serum transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / osmium / tranferrin / iron transport
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 / positive regulation of phosphorylation / clathrin-coated pit / 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 / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of iron ion transport / regulation of protein stability / HFE-transferrin receptor complex / recycling endosome / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / antibacterial humoral response / Clathrin-mediated endocytosis / iron ion transport / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / transmembrane transporter binding / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / 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-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
: / MALONATE ION / OSMIUM ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsWang, M. / Sun, H.
Funding support Hong Kong, China, 2items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)1733616P Hong Kong
National Science Foundation (NSF, China)21671203 China
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
DepositionJul 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)75,6334
Polymers75,2841
Non-polymers3483
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The peak at 45-50mL retention volume on a superdex-75 column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.831, 156.729, 107.313
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) / Plasmid details: Commercial / 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-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Os / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PIPES-NaOH 0.1M pH 6.6, disodium malonate 8mM, glycerol 18%, PEG 3350 17%

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen gas flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.14026 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2016
RadiationMonochromator: Graphite monochromer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14026 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 35884 / % possible obs: 100 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.025 / Rrim(I) all: 0.095 / Χ2: 0.99 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.66150.8523440.9090.2260.880.903100
2.66-2.73150.6923810.9310.1840.7140.917100
2.73-2.814.90.53523590.960.1430.5530.934100
2.8-2.88150.39523450.980.1050.4090.943100
2.88-2.9814.90.31623770.9850.0840.3270.951100
2.98-3.08150.25123610.9880.0670.260.996100
3.08-3.21150.18323750.9930.0490.1891.005100
3.21-3.3514.90.13723970.9960.0370.1420.995100
3.35-3.5314.90.11123590.9960.030.1151.004100
3.53-3.7514.90.09123990.9980.0240.0940.991100
3.75-4.0414.80.08424010.9970.0230.0870.989100
4.04-4.4514.80.08623820.9970.0230.0891.217100
4.45-5.0914.60.09524260.9970.0260.0981.502100
5.09-6.4114.30.07324420.9970.020.0760.945100
6.41-100140.04825360.9980.0130.050.55699.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260:000refinement
PDB_EXTRACT3.24data extraction
HKL-20001data reduction
PHASER2.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1B

4x1b


Resolution: 2.601→48.852 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8
RfactorNum. reflection% reflection
Rfree0.2286 1878 5.29 %
Rwork0.1972 --
obs0.1989 35513 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.29 Å2 / Biso mean: 54.2353 Å2 / Biso min: 20.25 Å2
Refinement stepCycle: final / Resolution: 2.601→48.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 9 28 4994
Biso mean--53.48 47.72 -
Num. residues----649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6015-2.67180.311260.2521220385
2.6718-2.75040.27221370.2428254298
2.7504-2.83920.26041540.22632562100
2.8392-2.94060.2541200.2312617100
2.9406-3.05840.28861530.22862606100
3.0584-3.19750.28011280.21952602100
3.1975-3.36610.23871370.2052636100
3.3661-3.57690.24361520.19392592100
3.5769-3.8530.19061540.18742618100
3.853-4.24050.19741400.16862612100
4.2405-4.85370.18971580.15682638100
4.8537-6.11320.21871610.19312652100
6.1132-48.8520.22651580.2025275599
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)
12.34860.2430.35951.50030.42513.13170.00440.4150.1507-0.3193-0.0610.0501-0.09260.01150.01820.35290.0737-0.01240.473-0.00560.084713.00686.5043-17.7094
20.42460.0740.01790.71940.19181.55380.1321-0.08160.10010.133-0.13490.089-0.2234-0.0976-0.03420.3842-0.07530.0650.5318-0.05180.075415.322717.808912.2955
36.55431.07650.61574.5174-0.0066.6368-0.29030.2210.1688-0.31780.03650.544-0.2732-0.60270.21860.46740.1247-0.0240.4078-0.01270.14845.035514.8103-15.5641
40.7210.7536-0.64641.8992-0.88381.21280.2184-0.11420.13350.2746-0.2987-0.3525-0.50660.61180.10440.5721-0.21350.07250.68110.02110.243633.288134.7218-1.9116
51.68910.6689-1.57361.614-2.00342.99820.2846-0.06290.30940.5446-0.07240.3178-0.4089-0.1474-0.24780.7597-0.22140.08770.57690.03270.257835.750853.7983-13.6183
63.07240.48090.16962.1553-0.771.28690.2863-0.22080.46920.6178-0.2269-0.1697-0.66880.5079-0.02330.9326-0.38380.10750.87740.02550.388933.355141.24573.012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 53 )A3 - 53
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 259 )A54 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 294 )A260 - 294
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 447 )A295 - 447
5X-RAY DIFFRACTION5chain 'A' and (resid 448 through 590 )A448 - 590
6X-RAY DIFFRACTION6chain 'A' and (resid 591 through 679 )A591 - 679

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