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- PDB-3qyt: Diferric bound human serum transferrin -

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Basic information

Entry
Database: PDB / ID: 3qyt
TitleDiferric bound human serum transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / diferric / human transferrin / intermediate / iron transporter
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
CARBONATE ION / : / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, N. / Zhang, H. / Wang, M. / Hao, Q. / Sun, H.
CitationJournal: Sci Rep / Year: 2012
Title: Iron and bismuth bound human serum transferrin reveals a partially-opened conformation in the N-lobe
Authors: Yang, N. / Zhang, H. / Wang, M. / Hao, Q. / Sun, H.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references / Other / Structure summary
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)76,0558
Polymers75,2841
Non-polymers7707
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.845, 90.435, 112.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules A

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


Mass: 75284.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P02787
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 13 molecules

#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.: 2 / Source method: obtained synthetically / Formula: CO3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.61 % / Mosaicity: 0.656 °
Crystal growTemperature: 271 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.01M HEPES, 15% PEG3000, pH 7.4, vapor diffusion, sitting drop, temperature 271K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17765 / % possible obs: 92.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.106 / Χ2: 1.031 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.92.60.52414470.979177.4
2.9-3.023.50.48917590.96194
3.02-3.154.60.42718350.944196.7
3.15-3.325.40.31418240.97196.8
3.32-3.536.10.25518210.981196.4
3.53-3.86.40.15917971.048195.8
3.8-4.186.50.11218211.147195.4
4.18-4.796.50.08218191.02194.4
4.79-6.036.50.07918091.073193.2
6.03-506.40.04718331.066189

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAV, 1JNF

2hav

1jnf


Resolution: 2.8→40.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.797 / SU B: 36.579 / SU ML: 0.342 / SU R Cruickshank DPI: 0.3832 / SU Rfree: 0.4541 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27498 908 5.1 %RANDOM
Rwork0.20616 ---
obs0.20958 16769 92.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 107.65 Å2 / Biso mean: 57.136 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5265 0 43 8 5316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225444
X-RAY DIFFRACTIONr_bond_other_d0.0010.023712
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9647372
X-RAY DIFFRACTIONr_angle_other_deg0.83839053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74424.571245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86215917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6831526
X-RAY DIFFRACTIONr_chiral_restr0.0640.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021076
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.13353382
X-RAY DIFFRACTIONr_mcbond_other0.3251375
X-RAY DIFFRACTIONr_mcangle_it3.466105408
X-RAY DIFFRACTIONr_scbond_it2.11552062
X-RAY DIFFRACTIONr_scangle_it3.399101964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 52 -
Rwork0.347 962 -
obs--72.9 %
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)
13.289-2.1079-0.67015.45222.4928.22180.1490.39290.6114-0.53150.1856-0.0165-1.43540.8636-0.33450.7293-0.26860.16610.47970.11550.475452.53916.3773-13.2364
21.06390.6886-1.1659-0.25930.59387.6803-0.11350.15290.0464-0.13350.1992-0.1412-0.32750.2568-0.08570.2506-0.03380.02590.12910.0050.251741.04299.80576.075
32.1094-0.84343.19596.7836-1.40859.30140.15950.13540.9391-0.378-0.2584-0.4053-0.93540.75530.09890.3642-0.04190.08120.2502-0.01340.415239.269220.005222.7056
48.05710.78261.3395.6666-1.70334.09150.39440.35151.5661-0.4377-0.406-0.8628-0.68951.27690.01170.27810.01880.14960.7580.13880.489550.902611.872622.9021
50.7330.8849-2.53870.8759-1.20567.54-0.15290.1680.0068-0.46010.0903-0.11550.9729-0.22460.06260.34610.08060.02560.2458-0.03550.237240.43672.436513.3343
65.7092-0.5757-1.76263.21091.14537.7146-0.1995-0.14780.0743-0.10840.2207-0.1262-0.52860.5162-0.02110.2761-0.0921-0.01360.08020.09560.192443.09869.23960.0727
72.71310.39510.87583.42790.93263.09320.032-0.5476-0.02070.0937-0.06770.1682-0.1114-0.31520.03560.13290.0174-0.02310.25540.11190.117912.382-4.94191.4355
83.3301-0.36610.54082.89740.19294.07430.09590.0065-0.472-0.1008-0.0375-0.03880.3534-0.0966-0.05840.12930.0039-0.02660.07260.06860.162412.5238-15.846-12.4809
913.4565-1.5226-0.69224.87890.10585.03050.221-1.3039-0.07780.3027-0.14290.922-0.0839-1.0958-0.07810.40060.09170.02090.55160.04520.29525.5282-0.390210.6509
105.15070.9510.672.2227-0.61441.75110.1674-0.7295-0.47540.2549-0.1179-0.35410.18370.1077-0.04950.2904-0.0415-0.06740.27260.08340.263421.8104-9.36733.6774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION2A50 - 112
3X-RAY DIFFRACTION3A113 - 166
4X-RAY DIFFRACTION4A167 - 215
5X-RAY DIFFRACTION5A216 - 260
6X-RAY DIFFRACTION6A261 - 340
7X-RAY DIFFRACTION7A341 - 443
8X-RAY DIFFRACTION8A444 - 585
9X-RAY DIFFRACTION9A586 - 625
10X-RAY DIFFRACTION10A626 - 679

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