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- PDB-1jqf: Human Transferrin N-Lobe Mutant H249Q -

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Basic information

Entry
Database: PDB / ID: 1jqf
TitleHuman Transferrin N-Lobe Mutant H249Q
ComponentsTRANSFERRIN
KeywordsTRANSPORT PROTEIN / iron binding protein
Function / homology
Function and homology information


iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / iron ion transport / Iron uptake and transport / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / regulation of protein stability / 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) / antibacterial humoral response / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / transmembrane transporter binding / intracellular iron ion homeostasis / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / 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 / Transferrin-like domain / 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 / Transferrin-like domain / 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBaker, H.M. / Mason, A.B. / He, Q.-Y. / MacGillivray, R.T.A. / Baker, E.N.
CitationJournal: Biochemistry / Year: 2001
Title: Ligand variation in the transferrin family: the crystal structure of the H249Q mutant of the human transferrin N-lobe as a model for iron binding in insect transferrins.
Authors: Baker, H.M. / Mason, A.B. / He, Q.Y. / MacGillivray, R.T. / Baker, E.N.
History
DepositionAug 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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.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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 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: TRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0474
Polymers36,8921
Non-polymers1553
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.2, 57.2, 135.75
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSFERRIN / SIDEROPHILIN


Mass: 36891.945 Da / Num. of mol.: 1 / Fragment: N-TERMINUS (Residues 20-353) / Mutation: H249Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNUT / Cell (production host): Kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02787
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Hanging drop. Protein solution 35 mg/ml protein in 0.1M ammonium bicarbonate pH 7.4. Reservoir solution 0.1M potassium acetate, pH 7.4, 20-25% PEG 3350. Equal volumes of protein and ...Details: Hanging drop. Protein solution 35 mg/ml protein in 0.1M ammonium bicarbonate pH 7.4. Reservoir solution 0.1M potassium acetate, pH 7.4, 20-25% PEG 3350. Equal volumes of protein and reservoir solutions mixed., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlprotein1drop
20.1 Mpotassium acetate1reservoir
320-25 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2000 / Details: mirrors
RadiationMonochromator: TR mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 30081 / % possible obs: 99.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 17
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2847 / % possible all: 96.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 30081
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A8E

1a8e


Resolution: 1.85→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 1426 random
Rwork0.221 --
obs-28873 -
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 6 192 2744
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.25
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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