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- PDB-1de4: HEMOCHROMATOSIS PROTEIN HFE COMPLEXED WITH TRANSFERRIN RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1de4
TitleHEMOCHROMATOSIS PROTEIN HFE COMPLEXED WITH TRANSFERRIN RECEPTOR
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HEMOCHROMATOSIS PROTEIN
  • TRANSFERRIN RECEPTOR
KeywordsMETAL TRANSPORT INHIBITOR/RECEPTOR / HFE / HEREDITARY HEMOCHROMATOSIS / MHC CLASS I / TRANSFERRIN RECEPTOR / METAL TRANSPORT INHIBITOR-RECEPTOR COMPLEX
Function / homology
Function and homology information


negative regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I / response to iron ion starvation / transferrin receptor activity / negative regulation of T cell cytokine production / hormone biosynthetic process / negative regulation of mitochondrial fusion / negative regulation of CD8-positive, alpha-beta T cell activation / transferrin transport / co-receptor binding / Transferrin endocytosis and recycling ...negative regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I / response to iron ion starvation / transferrin receptor activity / negative regulation of T cell cytokine production / hormone biosynthetic process / negative regulation of mitochondrial fusion / negative regulation of CD8-positive, alpha-beta T cell activation / transferrin transport / co-receptor binding / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / regulation of protein localization to cell surface / basal part of cell / positive regulation of signaling receptor activity / 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 / positive regulation of peptide hormone secretion / positive regulation of SMAD protein signal transduction / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of bone resorption / BMP signaling pathway / beta-2-microglobulin binding / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / negative regulation of signaling receptor activity / positive regulation of B cell proliferation / Hsp70 protein binding / RAC1 GTPase cycle / negative regulation of ubiquitin-dependent protein catabolic process / response to nutrient / osteoclast differentiation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / cellular response to leukemia inhibitory factor / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / acute-phase response / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / clathrin-coated endocytic vesicle membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / positive regulation of protein-containing complex assembly / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / receptor internalization / T cell mediated cytotoxicity / recycling endosome / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / positive regulation of protein localization to nucleus / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / double-stranded RNA binding
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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Aminopeptidase / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 3-Layer(bba) Sandwich / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transferrin receptor protein 1 / Beta-2-microglobulin / Hereditary hemochromatosis protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsBennett, M.J. / Lebron, J.A. / Bjorkman, P.J.
CitationJournal: Nature / Year: 2000
Title: Crystal structure of the hereditary haemochromatosis protein HFE complexed with transferrin receptor.
Authors: Bennett, M.J. / Lebron, J.A. / Bjorkman, P.J.
History
DepositionNov 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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_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_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOCHROMATOSIS PROTEIN
B: BETA-2-MICROGLOBULIN
C: TRANSFERRIN RECEPTOR
D: HEMOCHROMATOSIS PROTEIN
E: BETA-2-MICROGLOBULIN
F: TRANSFERRIN RECEPTOR
G: HEMOCHROMATOSIS PROTEIN
H: BETA-2-MICROGLOBULIN
I: TRANSFERRIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,56116
Polymers347,6859
Non-polymers8767
Water1629
1
A: HEMOCHROMATOSIS PROTEIN
B: BETA-2-MICROGLOBULIN
C: TRANSFERRIN RECEPTOR
D: HEMOCHROMATOSIS PROTEIN
E: BETA-2-MICROGLOBULIN
F: TRANSFERRIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,31210
Polymers231,7906
Non-polymers5234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16110 Å2
ΔGint-74 kcal/mol
Surface area79400 Å2
MethodPISA
2
G: HEMOCHROMATOSIS PROTEIN
H: BETA-2-MICROGLOBULIN
I: TRANSFERRIN RECEPTOR
hetero molecules

G: HEMOCHROMATOSIS PROTEIN
H: BETA-2-MICROGLOBULIN
I: TRANSFERRIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,49612
Polymers231,7906
Non-polymers7076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)110.4, 144.4, 327.1
Angle α, β, γ (deg.)90.0, 93.6, 90.0
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 9 molecules ADGBEHCFI

#1: Protein HEMOCHROMATOSIS PROTEIN / HFE


Mass: 32339.434 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBJ5-GS / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q30201
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P61769
#3: Protein TRANSFERRIN RECEPTOR /


Mass: 71807.258 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PACGP67A / Cell (production host): HIGH 5 INSECT CELLS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P02786

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Sugars , 1 types, 3 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 3 types, 13 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 3.74 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, TRIS, TRIMETHYLAMINE HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-8 %PEG80001reservoir
2200 mMTris-HCl1reservoir
310 mMtrimethylamine HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 122846 / Num. obs: 122846 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.5refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→30 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 685830.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: SEVERAL SIDECHAINS ARE MODELED AS ALA AS IN UNCOMPLEXED HFE. A POSITIVE DIFFERENCE PEAK NEAR TFR CHAINS C,F,I WHICH LACKED PROTEIN LIGANDS WAS MODELED AS A WATER MOLECULE (WATERS 4,6,8). A ...Details: SEVERAL SIDECHAINS ARE MODELED AS ALA AS IN UNCOMPLEXED HFE. A POSITIVE DIFFERENCE PEAK NEAR TFR CHAINS C,F,I WHICH LACKED PROTEIN LIGANDS WAS MODELED AS A WATER MOLECULE (WATERS 4,6,8). A POSITIVE DIFFERENCE PEAK NEAR THE HFE CHAIN G PLATFORM WAS MODELED AS A GLYCEROL. SEVERAL LOOPS HAVE RESIDUES WITH LOW CORRELATIONS AGAINST THE FINAL MAP: HFE PLATFORM LOOPS FROM STRAND 1 (S1) TO STRAND 2 (S2), S4-ALPHA1 HELIX; HFE ALPHA3 DOMAIN LOOPS S1-S2, S3-S4,S6-S7; BETA-2-MICROGLOBULIN LOOPS S1-S2, S3-S4, S5-S6, C-TERMINUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 11868 10 %RANDOM
Rwork0.231 ---
obs0.231 118743 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.72 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 66.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å20 Å2-1.65 Å2
2--1.82 Å20 Å2
3---2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24255 0 51 9 24315
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.661.5
X-RAY DIFFRACTIONc_mcangle_it6.92
X-RAY DIFFRACTIONc_scbond_it7.022
X-RAY DIFFRACTIONc_scangle_it9.262.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 1876 10.2 %
Rwork0.354 16473 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CRY.PARAMCRY.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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