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- PDB-1cx8: CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1cx8
TitleCRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR
ComponentsTRANSFERRIN RECEPTOR PROTEIN
KeywordsMETAL TRANSPORT / HUMAN TRANSFERRIN RECEPTOR
Function / homology
Function and homology information


transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / positive regulation of B cell proliferation / clathrin-coated pit / Hsp70 protein binding / positive regulation of T cell proliferation / RAC1 GTPase cycle / cellular response to leukemia inhibitory factor / osteoclast differentiation / response to nutrient / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / receptor internalization / HFE-transferrin receptor complex / recycling endosome / positive regulation of protein localization to nucleus / recycling endosome membrane / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / double-stranded RNA binding / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain ...Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SAMARIUM (III) ION / Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsLawrence, C.M. / Ray, S. / Babyonyshev, M. / Galluser, R. / Borhani, D. / Harrison, S.C.
CitationJournal: Science / Year: 1999
Title: Crystal structure of the ectodomain of human transferrin receptor.
Authors: Lawrence, C.M. / Ray, S. / Babyonyshev, M. / Galluser, R. / Borhani, D.W. / Harrison, S.C.
History
DepositionAug 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Jul 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSFERRIN RECEPTOR PROTEIN
B: TRANSFERRIN RECEPTOR PROTEIN
C: TRANSFERRIN RECEPTOR PROTEIN
D: TRANSFERRIN RECEPTOR PROTEIN
E: TRANSFERRIN RECEPTOR PROTEIN
F: TRANSFERRIN RECEPTOR PROTEIN
G: TRANSFERRIN RECEPTOR PROTEIN
H: TRANSFERRIN RECEPTOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)581,90156
Polymers572,9848
Non-polymers8,91848
Water0
1
A: TRANSFERRIN RECEPTOR PROTEIN
B: TRANSFERRIN RECEPTOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,47514
Polymers143,2462
Non-polymers2,22912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-63 kcal/mol
Surface area48150 Å2
MethodPISA
2
C: TRANSFERRIN RECEPTOR PROTEIN
D: TRANSFERRIN RECEPTOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,47514
Polymers143,2462
Non-polymers2,22912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-65 kcal/mol
Surface area48120 Å2
MethodPISA
3
E: TRANSFERRIN RECEPTOR PROTEIN
F: TRANSFERRIN RECEPTOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,47514
Polymers143,2462
Non-polymers2,22912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-66 kcal/mol
Surface area48310 Å2
MethodPISA
4
G: TRANSFERRIN RECEPTOR PROTEIN
H: TRANSFERRIN RECEPTOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,47514
Polymers143,2462
Non-polymers2,22912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-65 kcal/mol
Surface area48270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.400, 216.900, 361.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TRANSFERRIN RECEPTOR PROTEIN /


Mass: 71622.961 Da / Num. of mol.: 8 / Fragment: RESIDUES 122-760
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PCMVTFR / Organ (production host): OVARY CELLS / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: P02786
#2: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 24
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
#3: Chemical...
ChemComp-SM / SAMARIUM (III) ION / Samarium


Mass: 150.360 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Sm

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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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2.4 M KCl 10 mM KPi 1.5% PEG 20K, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mM1dropKCl
2100 mM1dropNaCl
35 mMpotassium phosphate1drop
412.5 mg/mlprotein1drop
52.3-2.5 M1reservoirKCl
610 mMKPi1reservoir
71.5-2.0 %PEG60001reservoiror 1.2-2.0& PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.2→15 Å / Num. all: 110528 / Num. obs: 110528 / % possible obs: 82 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 2 % / Rmerge(I) obs: 0.337 / Num. unique all: 2143 / % possible all: 32
Reflection
*PLUS

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNSrefinement
DMphasing
RefinementResolution: 3.2→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 5494 -RANDOM
Rwork0.2434 ---
all-108836 --
obs-108836 79.2 %-
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40448 0 360 0 40808
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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