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- PDB-6ctc: Crystal structure of human transferrin bound to Triferic FPC iron... -

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Basic information

Entry
Database: PDB / ID: 6ctc
TitleCrystal structure of human transferrin bound to Triferic FPC iron pyrophosphate
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / iron / pyrophosphate / transferrin / triferic iron / FPC / transfusion / blood / plasma
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 ...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
CARBONATE ION / : / PYROPHOSPHATE 2- / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsEdwards, T.E. / Pratt, R.
CitationJournal: Biometals / Year: 2018
Title: Ferric pyrophosphate citrate: interactions with transferrin.
Authors: Pratt, R. / Handelman, G.J. / Edwards, T.E. / Gupta, A.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)75,6465
Polymers75,2991
Non-polymers3484
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.370, 90.160, 110.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 75298.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / Production host: 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-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Apo human transferrin (ProSpec pro-325 purified by Q-sepharose) at 56 mg/mL (0.76 mM) against Morpheus screen condition D4 12.5% PEG 1000, 12.5% PEG3350, 12.5% MPD, 0.02 M each 1,6- ...Details: Apo human transferrin (ProSpec pro-325 purified by Q-sepharose) at 56 mg/mL (0.76 mM) against Morpheus screen condition D4 12.5% PEG 1000, 12.5% PEG3350, 12.5% MPD, 0.02 M each 1,6-hexanediol, 1-butanol, RS-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 246352d4, unique puck ID suv0-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→34.376 Å / Num. obs: 23450 / % possible obs: 99.9 % / Redundancy: 7.038 % / Biso Wilson estimate: 55.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 0.967 / Net I/σ(I): 31.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.677.2480.4844.717130.9290.522100
2.67-2.747.2630.3785.9716520.9510.408100
2.74-2.827.250.2767.9416170.9690.298100
2.82-2.917.2450.2189.8315940.9820.234100
2.91-37.270.18111.6915140.9860.19599.9
3-3.117.210.13115.9814870.9920.141100
3.11-3.227.2280.119.7414230.9960.108100
3.22-3.367.1710.07525.213780.9970.081100
3.36-3.517.0990.05931.1913300.9980.064100
3.51-3.687.0710.04638.2212640.9990.05100
3.68-3.887.0450.0394412050.9990.042100
3.88-4.116.940.03348.9911510.9990.036100
4.11-4.396.8850.02955.6610840.9990.031100
4.39-4.756.8160.02661.4510220.9990.028100
4.75-5.26.8190.02662.639330.9990.028100
5.2-5.816.6270.02759.948590.9990.02999.9
5.81-6.716.620.02463.5276010.02699.9
6.71-8.226.5060.02171.0265210.023100
8.22-11.636.3220.01978.9151910.021100
11.63-34.3765.3410.01972.7729310.0293.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4h0w

4h0w


Resolution: 2.6→34.376 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.57
RfactorNum. reflection% reflection
Rfree0.2532 1204 5.14 %
Rwork0.1801 --
obs0.1838 23438 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.52 Å2 / Biso mean: 58.6775 Å2 / Biso min: 27.75 Å2
Refinement stepCycle: final / Resolution: 2.6→34.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 15 62 5103
Biso mean--103.76 45.02 -
Num. residues----673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.70420.39921330.267724272560100
2.7042-2.82720.33841110.242224512562100
2.8272-2.97620.32641480.234824312579100
2.9762-3.16250.31751180.235124472565100
3.1625-3.40650.31921450.203124272572100
3.4065-3.7490.27051230.176424842607100
3.749-4.29060.23181440.160224632607100
4.2906-5.40230.19851290.144525092638100
5.4023-34.3790.21071530.16172595274899
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)
11.52980.2073-1.20120.73410.41722.78360.0475-0.05540.13-0.13880.123-0.2692-0.08470.3856-0.07730.44720.01430.05840.43820.00940.515845.976711.23037.6382
21.91120.57711.39351.3780.99732.00550.2205-0.3052-0.18830.1489-0.13090.01140.2258-0.2555-0.06420.425-0.06250.00540.45020.05270.364114.7953-8.1786-1.9652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 316 )A3 - 316
2X-RAY DIFFRACTION2chain 'A' and (resid 317 through 679 )A317 - 679

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