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- PDB-3rl1: HIV RT derived peptide complexed to HLA-A*0301 -

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Basic information

Entry
Database: PDB / ID: 3rl1
TitleHIV RT derived peptide complexed to HLA-A*0301
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-3 alpha chain
  • RT313 peptide
KeywordsIMMUNE SYSTEM / HLA-A*0301 / CD8+ T cell immunity / HIV derived peptides
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / T cell receptor binding / negative regulation of receptor binding / 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 / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / RNA-directed DNA polymerase activity / 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 / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / peptide antigen binding / DNA integration / 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 / establishment of integrated proviral latency / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / specific granule lumen / RNA stem-loop binding / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / 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 / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / T cell receptor signaling pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / DNA recombination / protein homotetramerization / amyloid fibril formation / aspartic-type endopeptidase activity / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / endoplasmic reticulum membrane / Neutrophil degranulation
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 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / MHC classes I/II-like antigen recognition protein / 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. / 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, A alpha chain / Beta-2-microglobulin / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, S. / Liu, J. / Cheng, H. / Tan, S. / Qi, J. / Yan, J. / Gao, G.F.
CitationJournal: Mol.Immunol. / Year: 2011
Title: Structural basis of cross-allele presentation by HLA-A*0301 and HLA-A*1101 revealed by two HIV-derived peptide complexes
Authors: Zhang, S. / Liu, J. / Cheng, H. / Tan, S. / Qi, J. / Yan, J. / Gao, G.F.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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, A-3 alpha chain
B: Beta-2-microglobulin
C: RT313 peptide


Theoretical massNumber of molelcules
Total (without water)44,5213
Polymers44,5213
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-16 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.953, 71.082, 75.517
Angle α, β, γ (deg.)90.00, 106.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A-3 alpha chain / HLA-A*0301 / MHC class I antigen A*3


Mass: 31628.838 Da / Num. of mol.: 1 / Fragment: residues in UNP 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLAA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04439
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide RT313 peptide


Mass: 1013.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YV12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2010
RadiationMonochromator: Cu Kalpha anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33190 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.2 Å2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.073 / Num. unique all: 5211 / Rsym value: 0.354 / % possible all: 86.4

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Processing

Software
NameVersionClassification
DDTdata collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.491 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8409 / SU ML: 0.26 / σ(F): 0.13 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1570 5.03 %RANDOM
Rwork0.1852 ---
all0.1871 ---
obs0.1871 31225 92.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.771 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 82.87 Å2 / Biso mean: 31.7043 Å2 / Biso min: 14.15 Å2
Baniso -1Baniso -2Baniso -3
1-16.2289 Å2-0 Å20.8527 Å2
2---9.9994 Å20 Å2
3----6.2296 Å2
Refinement stepCycle: LAST / Resolution: 2→24.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 0 380 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013222
X-RAY DIFFRACTIONf_angle_d1.0454364
X-RAY DIFFRACTIONf_chiral_restr0.106445
X-RAY DIFFRACTIONf_plane_restr0.004576
X-RAY DIFFRACTIONf_dihedral_angle_d19.2731172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9998-2.06430.27691100.22272119222973
2.0643-2.13810.28311200.22372426254684
2.1381-2.22360.27811380.20562613275190
2.2236-2.32470.23261290.19122654278392
2.3247-2.44720.22031460.19852756290294
2.4472-2.60040.23621390.19722740287995
2.6004-2.80090.26131500.19952803295397
2.8009-3.08220.23731600.19192835299598
3.0822-3.52710.23171540.17862882303699
3.5271-4.43950.17011600.154729063066100
4.4395-24.49290.1841640.15692921308598
Refinement TLS params.Method: refined / Origin x: 10.6133 Å / Origin y: 0.397 Å / Origin z: 17.3515 Å
111213212223313233
T0.1507 Å20.0106 Å20.0002 Å2-0.1674 Å20.0017 Å2--0.1594 Å2
L0.1327 °20.0487 °2-0.0686 °2-0.4288 °20.0199 °2--0.1235 °2
S-0.0056 Å °0.0149 Å °0.0003 Å °-0.0149 Å °0.0093 Å °-0.0033 Å °-0.0115 Å °0.0001 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 274
2X-RAY DIFFRACTION1ALLB0 - 99
3X-RAY DIFFRACTION1ALLC1 - 9
4X-RAY DIFFRACTION1ALLA275 - 559
5X-RAY DIFFRACTION1ALLB100 - 380
6X-RAY DIFFRACTION1ALLC98 - 337

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