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- PDB-1a6z: HFE (HUMAN) HEMOCHROMATOSIS PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1a6z
TitleHFE (HUMAN) HEMOCHROMATOSIS PROTEIN
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HFE
KeywordsMHC CLASS I COMPLEX / HFE / HEREDITARY HEMOCHROMATOSIS / MHC CLASS I
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 / negative regulation of T cell cytokine production / hormone biosynthetic process / negative regulation of CD8-positive, alpha-beta T cell activation / co-receptor binding / Transferrin endocytosis and recycling / transferrin receptor binding / regulation of protein localization to cell surface / basal part of cell ...negative regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I / response to iron ion starvation / negative regulation of T cell cytokine production / hormone biosynthetic process / negative regulation of CD8-positive, alpha-beta T cell activation / co-receptor binding / Transferrin endocytosis and recycling / transferrin receptor binding / regulation of protein localization to cell surface / basal part of cell / positive regulation of signaling receptor activity / response to iron ion / positive regulation of peptide hormone secretion / positive regulation of SMAD protein signal transduction / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / BMP signaling pathway / beta-2-microglobulin binding / negative regulation of signaling receptor activity / negative regulation of ubiquitin-dependent protein catabolic process / 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 / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / recycling endosome / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / apical part of cell / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / cytoplasmic vesicle / protein refolding / early endosome membrane / protein homotetramerization / protein-containing complex assembly / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / early endosome / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / positive regulation of gene expression / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / 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 / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / Hereditary hemochromatosis protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLebron, J.A. / Bennett, M.J. / Vaughn, D.E. / Chirino, A.J. / Snow, P.M. / Mintier, G.A. / Feder, J.N. / Bjorkman, P.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the hemochromatosis protein HFE and characterization of its interaction with transferrin receptor.
Authors: Lebron, J.A. / Bennett, M.J. / Vaughn, D.E. / Chirino, A.J. / Snow, P.M. / Mintier, G.A. / Feder, J.N. / Bjorkman, P.J.
History
DepositionMar 4, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _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: HFE
B: BETA-2-MICROGLOBULIN
C: HFE
D: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)88,1754
Polymers88,1754
Non-polymers00
Water41423
1
A: HFE
B: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)44,0882
Polymers44,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-10 kcal/mol
Surface area18720 Å2
MethodPISA
2
C: HFE
D: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)44,0882
Polymers44,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-9 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.800, 100.100, 147.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.00324, 0.99996, -0.008301), (0.999973, -0.003186, 0.006559), (0.006533, -0.008322, -0.999944)-33.392, 33.554, 17.7
2given(-0.021022, 0.999737, 0.009124), (0.999776, 0.020998, 0.00272), (0.002527, 0.009179, -0.999955)-33.179, 32.036, 17.831

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Components

#1: Protein HFE


Mass: 32339.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HFE / Organ: OVARY / Cell line (production host): CHO / Cellular location (production host): SECRETED / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q30201
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: OVARY / References: UniProt: P61769
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.89 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 5.9 / Method: vapor diffusion, hanging drop
Details: drop contained 1:1 mixture of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
216 %(w/v)PEG40001reservoir
30.4 Mammonium acetate1reservoir
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.07
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 187780 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 67.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3 / % possible all: 97
Reflection
*PLUS
Num. obs: 32145 / Num. measured all: 188780
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.857refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CLR

2clr


Resolution: 2.6→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1555 4.9 %RANDOM
Rwork0.233 ---
obs0.233 31770 98.5 %-
Displacement parametersBiso mean: 63.2 Å2
Baniso -1Baniso -2Baniso -3
1--17.72 Å20 Å20 Å2
2---1.02 Å20 Å2
3---18.74 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6076 0 0 23 6099
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.131
X-RAY DIFFRACTIONx_mcangle_it6.331.5
X-RAY DIFFRACTIONx_scbond_it7.21.5
X-RAY DIFFRACTIONx_scangle_it9.932
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev Biso : 7.4 Å2 / Rms dev position: 0.02 Å / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 2.6→2.71 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.412 191 5 %
Rwork0.399 3665 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.857 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor obs: 0.399

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