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- PDB-7ffm: Human serum transferrin with five osmium binding sites -

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Basic information

Entry
Database: PDB / ID: 7ffm
TitleHuman serum transferrin with five osmium binding sites
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Transferrin / osmium / titanium
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 / ferrous iron binding / regulation of protein stability / 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
Similarity search - Domain/homology
TITANIUM ION / MALONATE ION / NITRILOTRIACETIC ACID / OSMIUM ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 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 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.ptnr1_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: 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)76,5779
Polymers75,2841
Non-polymers1,2928
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Peak near 45mL retention volume on a superdex-75 column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-4 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.954, 158.211, 107.102
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: 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 , 5 types, 20 molecules

#2: Chemical ChemComp-4TI / TITANIUM ION


Mass: 47.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ti
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO6
#5: Chemical
ChemComp-OS / OSMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsThe I429V mutation is inherit from the MR model and ultimately from 2HAV

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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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PIPES-Na 100mM pH 6.5, di-sodium malonate 8mM, PEG3350 17%, glycerol 18%
PH range: 6.4-7.2 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cold nitrogen gas flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.14026 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2016
RadiationMonochromator: graphite filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14026 Å / Relative weight: 1
ReflectionResolution: 3.06→100 Å / Num. obs: 26385 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.03 / Rrim(I) all: 0.085 / Χ2: 0.94 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.06-3.128.20.44312880.9520.1640.4730.942100
3.12-3.198.20.34613160.9690.1280.3690.931100
3.19-3.278.30.26612830.9830.0980.2840.952100
3.27-3.358.20.22513100.9820.0830.240.948100
3.35-3.448.20.17612890.9890.0650.1880.909100
3.44-3.548.20.15113170.9920.0560.1610.939100
3.54-3.658.20.11413100.9950.0420.1220.86199.9
3.65-3.788.20.10212960.9960.0380.1080.966100
3.78-3.948.20.08213350.9970.0310.0880.823100
3.94-4.118.20.06513050.9980.0240.070.726100
4.11-4.338.20.05813190.9980.0220.0620.691100
4.33-4.68.10.05813230.9970.0220.0620.761100
4.6-4.968.10.06913340.9970.0250.0741.056100
4.96-5.468.10.08613240.9940.0320.0911.532100
5.46-6.2580.08913480.9920.0330.0951.645100
6.25-7.877.70.05313530.9970.020.0570.81100
7.87-1007.70.03814210.9980.0150.0410.46499.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260:000refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASER2.7.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1B

4x1b


Resolution: 3.06→46.77 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.11
RfactorNum. reflection% reflection
Rfree0.2117 1156 5.17 %
Rwork0.1795 --
obs0.1801 22374 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.3 Å2 / Biso mean: 53.0017 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 3.06→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 26 12 5036
Biso mean--79.22 60.22 -
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 (%)
3.0601-3.19930.26071430.2253254398
3.1993-3.36790.23291390.19172641100
3.3679-3.57890.22181370.18182636100
3.5789-3.85510.19221560.16282626100
3.8551-4.24280.18011320.14872640100
4.2428-4.85620.17821460.14782666100
4.8562-6.11610.20691560.18882678100
6.1161-46.770.24071470.20562788100
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)
12.00450.3606-0.42730.6338-0.01852.97280.01250.2684-0.0675-0.133-0.0265-0.0510.0721-0.0495-0.04130.50530.07220.00990.1562-0.02020.0717-15.3946-10.3907-13.1841
20.55750.1481-0.14050.6816-0.64792.46650.1147-0.1551-0.14720.1908-0.1989-0.12290.31730.2158-0.01690.5511-0.0854-0.05280.20830.06170.1036-14.5064-18.458316.6155
34.98150.7002-0.31344.9591.54394.6683-0.07530.1944-0.2219-0.27390.1331-0.5835-0.02330.4439-0.23370.5820.13890.01920.15250.00740.1616-5.0185-14.8301-15.6619
40.90781.19470.78542.54191.14281.03650.2998-0.1286-0.11230.2965-0.35020.29240.4898-0.54170.26590.719-0.1961-0.07670.3486-0.03940.2541-32.5898-37.636-3.6335
52.19250.95261.00022.13871.67062.91310.217-0.0409-0.31620.40290.0433-0.30370.21240.0988-0.09680.8061-0.1921-0.06420.3018-0.04790.2615-37.9395-54.732-16.5809
60.72470.74220.71423.12431.29861.32980.2771-0.429-0.18260.7785-0.24430.11450.7114-0.4224-0.01371.0651-0.3702-0.06690.6378-0.02840.3563-33.5549-43.72752.5169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 93 )A3 - 93
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 259 )A94 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 294 )A260 - 294
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 471 )A295 - 471
5X-RAY DIFFRACTION5chain 'A' and (resid 472 through 573 )A472 - 573
6X-RAY DIFFRACTION6chain 'A' and (resid 574 through 679 )A574 - 679

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