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- PDB-6bj2: TCR589 in complex with HIV(Pol448-456)/HLA-B35 -

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Basic information

Entry
Database: PDB / ID: 6bj2
TitleTCR589 in complex with HIV(Pol448-456)/HLA-B35
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HIV Pol B35 peptide
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • TCR 589 alpha chain
  • TCR 589 beta chain
KeywordsIMMUNE SYSTEM / agonist / complex
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / TAP binding / viral life cycle / 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 / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Assembly Of The HIV Virion / HIV-1 retropepsin / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / : / defense response / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / : / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / protein processing / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / host multivesicular body / 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 / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / RNA-directed DNA polymerase / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / viral genome integration into host DNA / peptide antigen binding / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / RNA-directed DNA polymerase activity / 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 / Interferon alpha/beta signaling / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / RNA-DNA hybrid ribonuclease activity / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / peptidase activity / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / Reverse transcriptase connection / Reverse transcriptase connection domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set 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. / Immunoglobulin V-set domain / 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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 / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Human nkt tcr beta chain / HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsJude, K.M. / Sibener, L.V. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103867 United States
CitationJournal: Cell / Year: 2018
Title: Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding.
Authors: Sibener, L.V. / Fernandes, R.A. / Kolawole, E.M. / Carbone, C.B. / Liu, F. / McAffee, D. / Birnbaum, M.E. / Yang, X. / Su, L.F. / Yu, W. / Dong, S. / Gee, M.H. / Jude, K.M. / Davis, M.M. / ...Authors: Sibener, L.V. / Fernandes, R.A. / Kolawole, E.M. / Carbone, C.B. / Liu, F. / McAffee, D. / Birnbaum, M.E. / Yang, X. / Su, L.F. / Yu, W. / Dong, S. / Gee, M.H. / Jude, K.M. / Davis, M.M. / Groves, J.T. / Goddard III, W.A. / Heath, J.R. / Evavold, B.D. / Vale, R.D. / Garcia, K.C.
History
DepositionNov 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Dec 11, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 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

Downloads & links

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Assembly

Deposited unit
D: TCR 589 alpha chain
E: TCR 589 beta chain
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: HIV Pol B35 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,01710
Polymers95,1755
Non-polymers8425
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-116 kcal/mol
Surface area38280 Å2
Unit cell
Length a, b, c (Å)156.480, 59.280, 123.570
Angle α, β, γ (deg.)90.00, 110.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules DEAB

#1: Protein TCR 589 alpha chain


Mass: 23278.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6IRV4
#2: Protein TCR 589 beta chain


Mass: 27194.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: K7N5M4
#3: Protein HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30685, UniProt: P01889*PLUS
#4: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#5: Protein/peptide HIV Pol B35 peptide


Mass: 1014.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS

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Sugars , 2 types, 2 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 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.: 1
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 , 2 types, 4 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Tris, pH 8.0, 20% PEG3350, 0.002 M zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 15094 / % possible obs: 97.03 % / Redundancy: 3.3 % / Biso Wilson estimate: 102.67 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1116 / Rpim(I) all: 0.07175 / Rrim(I) all: 0.1333 / Net I/σ(I): 8.96
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7365 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1439 / CC1/2: 0.795 / Rpim(I) all: 0.489 / Rrim(I) all: 0.889 / % possible all: 94.02

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1A1N, 2AK4, 4JRY

1a1n

2ak4

4jry


Resolution: 3.35→42.756 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 708 4.69 %random
Rwork0.2453 ---
obs0.2467 15083 97.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→42.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 45 1 6445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056629
X-RAY DIFFRACTIONf_angle_d0.5419045
X-RAY DIFFRACTIONf_dihedral_angle_d14.2093883
X-RAY DIFFRACTIONf_chiral_restr0.042985
X-RAY DIFFRACTIONf_plane_restr0.0041184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.60850.35471370.32342790X-RAY DIFFRACTION96
3.6085-3.97140.32531400.2972910X-RAY DIFFRACTION99
3.9714-4.54560.27191450.24882836X-RAY DIFFRACTION96
4.5456-5.72480.28341420.21952896X-RAY DIFFRACTION98
5.7248-42.760.23581440.22462943X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.00121.42531.04053.2953-0.577410.80850.0012-0.28120.13530.0142-0.3951-0.367-0.75734.04560.14890.4821-0.26580.05682.10770.10160.8396-20.5989-22.1405111.3798
25.8271-0.5129-3.23693.1250.76491.5374-0.00270.4020.1677-0.6628-0.8722-0.3942-0.23471.0440.63191.065-0.09320.05252.04170.23981.0146-8.3631-21.857877.0841
31.442-1.47080.31220.5729-1.16823.08460.2691-0.22090.2371-0.2351-0.171-0.0915-2.34251.1176-0.05961.3363-0.9330.09041.92870.17071.1672-18.362-6.120990.0874
44.64252.79982.33886.7617-1.25712.82810.2914-0.9462-0.69151.489-0.52580.4693-0.8203-0.04040.24130.5781-0.38260.15382.53380.16240.9509-22.7782-23.5707118.504
50.41480.85850.54552.4059-0.13343.67030.33530.658-0.5381-0.3137-0.22870.10722.112.0791-0.19281.10610.6455-0.03041.1703-0.05580.9316-28.8849-43.9514133.694
62.44-2.7294-0.90953.9211-1.6493.21790.4782-0.029-0.7009-0.09340.32170.76550.95-0.5365-0.45021.0822-0.2252-0.26450.6530.23691.0966-40.484-52.4982164.2726
77.16320.94890.05783.58421.02426.6514-0.14910.2050.3671-0.11380.0925-0.1981-0.89211.02270.04060.7095-0.0191-0.08790.62590.00970.7575-35.644-22.3467138.3896
83.8984-0.32683.55516.1359-2.68344.12430.2193-0.9014-0.78010.16120.31320.33670.3934-0.7191-0.47590.82540.07290.07310.49860.0660.7105-37.6353-40.1036165.9848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:182
2X-RAY DIFFRACTION2chain A and resid 183:276
3X-RAY DIFFRACTION3chain B
4X-RAY DIFFRACTION4chain C
5X-RAY DIFFRACTION5chain D and resid 2:113
6X-RAY DIFFRACTION6chain D and resid 114:203
7X-RAY DIFFRACTION7chain E and resid 2:112
8X-RAY DIFFRACTION8chain E and resid 113:203

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