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- PDB-6cpo: Crystal structure of DR15 presenting the RQ13 peptide -

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Basic information

Entry
Database: PDB / ID: 6cpo
TitleCrystal structure of DR15 presenting the RQ13 peptide
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA-DRB1 protein
  • RQ13
KeywordsIMMUNE SYSTEM / IMMUNE RECEPTOR
Function / homology
Function and homology information


host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / integrase activity / intermediate filament / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / humoral immune response / macrophage differentiation / Generation of second messenger molecules / negative regulation of type II interferon production / immunological synapse / PD-1 signaling / epidermis development / Binding and entry of HIV virion / negative regulation of inflammatory response to antigenic stimulus / viral life cycle / negative regulation of T cell proliferation / Membrane binding and targetting of GAG proteins / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Assembly Of The HIV Virion / clathrin-coated endocytic vesicle membrane / HIV-1 retropepsin / : / ER to Golgi transport vesicle membrane / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / : / exoribonuclease H activity / structural constituent of cytoskeleton / protein processing / cognition / host multivesicular body / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / RNA-directed DNA polymerase / peptide antigen binding / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of T cell activation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / peptidase activity / T cell receptor signaling pathway / early endosome membrane / viral nucleocapsid / positive regulation of canonical NF-kappaB signal transduction / DNA recombination / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / Hydrolases; Acting on ester bonds / lysosome
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Gag protein p6 ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / 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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / MHC classes I/II-like antigen recognition protein / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFarenc, C. / Gras, S. / Rossjohn, J.
CitationJournal: Sci Immunol / Year: 2018
Title: CD4+T cell-mediated HLA class II cross-restriction in HIV controllers.
Authors: Galperin, M. / Farenc, C. / Mukhopadhyay, M. / Jayasinghe, D. / Decroos, A. / Benati, D. / Tan, L.L. / Ciacchi, L. / Reid, H.H. / Rossjohn, J. / Chakrabarti, L.A. / Gras, S.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA-DRB1 protein
C: RQ13
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA-DRB1 protein
F: RQ13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,94613
Polymers89,7216
Non-polymers1,2257
Water5,008278
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA-DRB1 protein
C: RQ13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5487
Polymers44,8603
Non-polymers6884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-28 kcal/mol
Surface area18520 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA-DRB1 protein
F: RQ13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3986
Polymers44,8603
Non-polymers5373
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-31 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.740, 73.500, 94.940
Angle α, β, γ (deg.)90.00, 106.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21185.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA-DRB1 protein / / MHC class II antigen


Mass: 22073.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: D7RIH9, UniProt: P01911*PLUS

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Protein/peptide / Sugars , 2 types, 6 molecules CF

#3: Protein/peptide RQ13 / Pr55Gag


Mass: 1600.797 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_HXB2R (virus) / References: UniProt: P04591, UniProt: P04585*PLUS
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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, 281 molecules

#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PBS pH 7.5, Na acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→48.2 Å / Num. obs: 34562 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 40.08 Å2 / Rpim(I) all: 0.076 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 3604 / Rpim(I) all: 0.408

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDO

4mdo


Resolution: 2.4→47.08 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.442 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.438 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1707 4.94 %RANDOM
Rwork0.203 ---
obs0.205 34562 100 %-
Displacement parametersBiso mean: 33.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.7407 Å20 Å21.101 Å2
2---3.4899 Å20 Å2
3----1.2508 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.4→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 80 278 6635
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076540HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.998905HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2238SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes940HARMONIC5
X-RAY DIFFRACTIONt_it6540HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion18.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7191SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.285 166 5.56 %
Rwork0.235 2818 -
all0.238 2984 -
obs--99.93 %

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