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- PDB-6cqn: Crystal structure of F5 TCR -DR11-RQ13 peptide complex -

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Basic information

Entry
Database: PDB / ID: 6cqn
TitleCrystal structure of F5 TCR -DR11-RQ13 peptide complex
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • F5 alpha chain
  • F5 beta chain
  • Peptide from Capsid protein p24
KeywordsIMMUNE SYSTEM / TCR / IMMUNE RECEPTOR
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 T cell mediated immune response to tumor cell / 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 kinase activity / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / intermediate filament / T cell receptor complex / polysaccharide binding / T-helper 1 type immune response / transport vesicle membrane / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / APOBEC3G mediated resistance to HIV-1 infection / macrophage differentiation / negative regulation of type II interferon production / humoral immune response / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / Binding and entry of HIV virion / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / viral life cycle / MHC class II antigen presentation / Membrane binding and targetting of GAG proteins / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / negative regulation of inflammatory response to antigenic stimulus / response to bacterium / protein tetramerization / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / Assembly Of The HIV Virion / exoribonuclease H / clathrin-coated endocytic vesicle membrane / exoribonuclease H activity / ER to Golgi transport vesicle membrane / Budding and maturation of HIV virion / protein processing / structural constituent of cytoskeleton / host multivesicular body / cognition / peptide antigen assembly with MHC class II protein complex / viral genome integration into host DNA / MHC class II protein complex / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / positive regulation of T cell mediated cytotoxicity / RNA stem-loop binding / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / RNA-directed DNA polymerase activity / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / RNA-DNA hybrid ribonuclease activity / positive regulation of T cell activation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / adaptive immune response
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 ...: / 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 / : / Immunoglobulin V-Type / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Immunoglobulin V-set 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 / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / MHC classes I/II-like antigen recognition protein / Retropepsin-like catalytic domain / Immunoglobulin V-set domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 24 / T cell receptor beta constant 2 / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Gag-Pol polyprotein / Gag polyprotein / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 15, 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
Revision 1.4Nov 6, 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 II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-11 beta chain
C: Peptide from Capsid protein p24
D: F5 alpha chain
E: F5 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,74114
Polymers95,8195
Non-polymers9229
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14790 Å2
ΔGint-114 kcal/mol
Surface area38100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.317, 205.792, 70.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB

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


Mass: 21185.930 Da / Num. of mol.: 1
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 class II histocompatibility antigen, DRB1-11 beta chain / DR-5 / DR5 / DRw11 / MHC class II antigen DRB1*11


Mass: 22246.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P20039, UniProt: P01911*PLUS

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Protein , 2 types, 2 molecules DE

#4: Protein F5 alpha chain


Mass: 22801.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: A0A0B4J272*PLUS
#5: Protein F5 beta chain


Mass: 27984.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: A0A0G2JMB4*PLUS

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Protein/peptide / Sugars , 2 types, 3 molecules C

#3: Protein/peptide Peptide from Capsid protein p24 / Pr55Gag


Mass: 1600.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Gene: gag / Production host: Homo sapiens (human) / References: UniProt: P04591, UniProt: P04585*PLUS
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 4 types, 139 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: MgCl, Am SO4,PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.5→45.96 Å / Num. obs: 38652 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 55.81 Å2 / Rpim(I) all: 0.056 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 4320 / Rpim(I) all: 0.415

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDO, 1KGC

4mdo

1kgc


Resolution: 2.5→42.48 Å / Cor.coef. Fo:Fc: 0.9347 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.384 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.385 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 2003 5.18 %RANDOM
Rwork0.1958 ---
obs0.1986 38652 99.98 %-
Displacement parametersBiso mean: 50.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.3991 Å20 Å20 Å2
2---4.6424 Å20 Å2
3---4.2433 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: 1 / Resolution: 2.5→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 51 132 6878
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096925HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.19419HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2332SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes194HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1000HARMONIC5
X-RAY DIFFRACTIONt_it6925HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion20.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion875SEMIHARMONIC5
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_contact7570SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.3148 139 4.7 %
Rwork0.2565 2820 -
all0.2593 2959 -
obs--99.98 %

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