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- PDB-6jas: Human serum transferrin with iron citrate bound -

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Basic information

Entry
Database: PDB / ID: 6jas
TitleHuman serum transferrin with iron citrate bound
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Transferrin / iron
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
Similarity search - Domain/homology
CITRIC ACID / : / MALONATE ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsWang, M. / Wang, H. / Sun, H.
CitationJournal: To Be Published
Title: Binding of ruthenium and osmium at non-iron sites of transferrin explains their iron-independent cellular uptake
Authors: Wang, M. / Wang, H. / Sun, H.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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)75,6905
Polymers75,2841
Non-polymers4064
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Discard >150kDa fractions
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.567, 157.153, 107.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

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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.: 2 / 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.82 Å3/Da / Density % sol: 67.82 % / Description: Pale red half-moon shaped large crystals
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.6
Details: PIPES-NaOH 0.1M pH 6.6, di-sodium malonate 8 mM, glycerol 18%, PEG3350 17%
PH range: 6.5-7.2 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.14026 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2016
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14026 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 40122 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.035 / Rrim(I) all: 0.103 / Χ2: 0.955 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.568.50.76926370.8990.2780.8190.877100
2.56-2.628.70.64926610.9160.2320.6890.897100
2.62-2.698.70.50726150.9510.1820.5390.924100
2.69-2.778.70.40826600.9640.1460.4340.953100
2.77-2.868.70.3126430.9760.1110.3290.98100
2.86-2.968.70.25226530.9830.0910.2680.986100
2.96-3.088.70.20126400.9870.0720.2141100
3.08-3.228.70.15126650.9920.0540.1611.003100
3.22-3.398.70.11926790.9930.0430.1260.947100
3.39-3.618.70.09926500.9950.0360.1060.917100
3.61-3.888.70.08726800.9950.0320.0930.909100
3.88-4.278.60.08926890.9940.0320.0951.02699.9
4.27-4.898.50.126870.9920.0370.1071.362100
4.89-6.178.40.09327320.9920.0340.0991.121100
6.17-1008.20.04828310.9980.0180.0520.42599.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1B

4x1b


Resolution: 2.501→47.578 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.23
RfactorNum. reflection% reflection
Rfree0.2186 2003 5.18 %
Rwork0.1888 --
obs0.1904 38649 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.53 Å2 / Biso mean: 48.8518 Å2 / Biso min: 17.28 Å2
Refinement stepCycle: final / Resolution: 2.501→47.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5047 0 22 75 5144
Biso mean--72.76 35.97 -
Num. residues----656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5012-2.56380.2956870.2451675176262
2.5638-2.63310.28781280.24462337246587
2.6331-2.71060.2621330.23442653278698
2.7106-2.7980.25721310.234327042835100
2.798-2.8980.25881560.218126932849100
2.898-3.01410.25551410.219626842825100
3.0141-3.15120.24741440.210527172861100
3.1512-3.31730.26571520.197926872839100
3.3173-3.52510.22131510.191927092860100
3.5251-3.79710.19041450.171727192864100
3.7971-4.17910.18451510.160927362887100
4.1791-4.78330.16241730.151227152888100
4.7833-6.02450.19941510.175727602911100
6.0245-47.58670.23641600.1862857301799
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)
13.47630.3581.15153.19770.13242.84350.07780.4639-0.0329-0.3535-0.1006-0.00880.1170.180.06070.23520.10160.01810.2745-0.06080.181913.02596.7144-17.765
20.78620.26820.27981.27940.60793.39420.1558-0.09470.0860.1045-0.25240.1107-0.1554-0.11030.07080.1618-0.05220.03780.2475-0.02120.265815.188317.889712.2651
30.51130.5061-0.26661.9397-0.13980.66840.1368-0.15030.1431-0.0721-0.2247-0.1577-0.31310.32050.07570.3478-0.07750.08590.39140.02680.308227.2330.6627-4.7843
41.98410.891-1.02931.6331-1.51732.42870.1982-0.08110.21340.3895-0.080.3302-0.3333-0.0379-0.12470.5165-0.19640.07890.36630.00590.364635.391453.9074-13.4666
55.2150.9098-0.38472.2373-0.23551.87810.0667-0.36340.4270.2357-0.1185-0.2276-0.12850.69160.0650.7092-0.3653-0.05770.80910.05590.480746.302440.44047.0778
63.3931.7321.00523.21690.10761.31840.3483-0.19360.48760.5506-0.17040.3516-0.32890.1274-0.1090.5862-0.20190.19860.47840.03060.441225.539542.70070.5248
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 447 )A260 - 447
4X-RAY DIFFRACTION4chain 'A' and (resid 448 through 590 )A448 - 590
5X-RAY DIFFRACTION5chain 'A' and (resid 591 through 633 )A591 - 633
6X-RAY DIFFRACTION6chain 'A' and (resid 634 through 679 )A634 - 679

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