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- PDB-3w39: Crystal structure of HLA-B*5201 in complexed with HIV immunodomin... -

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Basic information

Entry
Database: PDB / ID: 3w39
TitleCrystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-52 alpha chain
  • peptid from Gag-Pol polyprotein
KeywordsIMMUNE SYSTEM / Class I Major Histocompatibility Complex / MHC / Membrane
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / negative regulation of receptor binding ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / negative regulation of receptor binding / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / peptide antigen assembly with MHC class II protein complex / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / exoribonuclease H activity / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / defense response / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / host multivesicular body / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / DNA integration / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / Interferon alpha/beta signaling / viral penetration into host nucleus / Modulation by Mtb of host immune system / specific granule lumen / RNA stem-loop binding / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / RNA-DNA hybrid ribonuclease activity / MHC class II protein complex binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / host cell / protein-folding chaperone binding / negative regulation of neuron projection development / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / adaptive immune response / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / DNA-directed DNA polymerase activity / learning or memory / immune response / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / endoplasmic reticulum lumen / viral translational frameshifting / Golgi membrane / signaling receptor binding / lysosomal membrane
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb / MHC class I-like antigen recognition-like / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like superfamily / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. ...Yagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. / Mallal, S. / John, M. / Ose, T. / Matsubara, H. / Kanda, R. / Fukunaga, Y. / Honda, K. / Kawashima, Y. / Ariumi, Y. / Oka, S. / Maenaka, K. / Takiguchi, M.
CitationJournal: J.Virol. / Year: 2013
Title: Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity
Authors: Yagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. / Mallal, S. / John, M. / Ose, T. / Matsubara, H. ...Authors: Yagita, Y. / Kuse, N. / Kuroki, K. / Gatanaga, H. / Carlson, J.M. / Chikata, T. / Brumme, Z.L. / Murakoshi, H. / Akahoshi, T. / Pfeifer, N. / Mallal, S. / John, M. / Ose, T. / Matsubara, H. / Kanda, R. / Fukunaga, Y. / Honda, K. / Kawashima, Y. / Ariumi, Y. / Oka, S. / Maenaka, K. / Takiguchi, M.
History
DepositionDec 13, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 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: HLA class I histocompatibility antigen, B-52 alpha chain
B: Beta-2-microglobulin
C: peptid from Gag-Pol polyprotein
D: HLA class I histocompatibility antigen, B-52 alpha chain
E: Beta-2-microglobulin
F: peptid from Gag-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)89,7326
Polymers89,7326
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, B-52 alpha chain
B: Beta-2-microglobulin
C: peptid from Gag-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)44,8663
Polymers44,8663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-19 kcal/mol
Surface area19270 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, B-52 alpha chain
E: Beta-2-microglobulin
F: peptid from Gag-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)44,8663
Polymers44,8663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-20 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.045, 83.255, 170.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN D
12CHAIN B
22CHAIN E

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPROCHAIN AAA1 - 2771 - 277
21METMETPROPROCHAIN DDD1 - 2771 - 277
12ILEILEMETMETCHAIN BBB1 - 992 - 100
22ILEILEMETMETCHAIN EEE1 - 992 - 100

NCS ensembles :
ID
1
2

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Components

#1: Protein HLA class I histocompatibility antigen, B-52 alpha chain / HLA class I histocompatibility antigen heavy chain / Bw-52 / HLA class I histocompatibility antigen ...HLA class I histocompatibility antigen heavy chain / Bw-52 / HLA class I histocompatibility antigen / B-5 alpha chain / MHC class I antigen B*52


Mass: 32137.414 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30490, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide peptid from Gag-Pol polyprotein


Mass: 848.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic HIV-1 PEPTIDE
Source: (synth.) Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
References: UniProt: P12499
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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 31, 2012 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→46.9 Å / Num. all: 18422 / Num. obs: 18422 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 23.07 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 2.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2548 / % possible all: 98.2

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Processing

Software
NameVersionClassification
RAYONIXMX225HEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+28 / Resolution: 3.1→38.802 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.656 / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 38.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3469 912 5.15 %RANDOM
Rwork0.2952 ---
obs0.2979 17704 95.97 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.02 Å2 / Biso mean: 14.3983 Å2 / Biso min: 4.38 Å2
Refinement stepCycle: LAST / Resolution: 3.1→38.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 0 0 6312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146496
X-RAY DIFFRACTIONf_angle_d1.4848826
X-RAY DIFFRACTIONf_chiral_restr0.087906
X-RAY DIFFRACTIONf_plane_restr0.0061164
X-RAY DIFFRACTIONf_dihedral_angle_d17.3282396
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2267X-RAY DIFFRACTIONPOSITIONAL0.111
12D2267X-RAY DIFFRACTIONPOSITIONAL0.111
21B829X-RAY DIFFRACTIONPOSITIONAL0.124
22E829X-RAY DIFFRACTIONPOSITIONAL0.124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.26340.45351430.35542165230890
3.2634-3.46780.42351340.32012323245795
3.4678-3.73530.3641300.28962358248896
3.7353-4.11090.32491170.29382419253697
4.1109-4.70480.31641320.27872458259098
4.7048-5.92420.30251350.28512452258797
5.9242-38.8050.27391210.27222617273898

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