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- PDB-3vcl: Crystal Structure of HLA-B7 with the HCMV pp65 peptide RPHERNGFTVL -

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Basic information

Entry
Database: PDB / ID: 3vcl
TitleCrystal Structure of HLA-B7 with the HCMV pp65 peptide RPHERNGFTVL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • peptide from Tegument protein pp65
KeywordsIMMUNE SYSTEM / Class I Histocompatibility antigen / Antigen presentation / T-cell receptor / Membrane
Function / homology
Function and homology information


host cell viral assembly compartment / viral tegument / virion component => GO:0044423 / 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 ...host cell viral assembly compartment / viral tegument / virion component => GO:0044423 / 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 / detection of bacterium / HCMV Late Events / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / HCMV Early Events / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 / Beta-2-Microglobulin ...Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Tegument protein pp65 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / 65 kDa phosphoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPetersen, J. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2012
Title: The impact of a large and frequent deletion in the human TCR beta locus on antiviral immunity
Authors: Brennan, R.M. / Petersen, J. / Neller, M.A. / Miles, J.J. / Burrows, J.M. / Smith, C. / McCluskey, J. / Khanna, R. / Rossjohn, J. / Burrows, S.R.
History
DepositionJan 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-7 alpha chain
B: Beta-2-microglobulin
C: peptide from Tegument protein pp65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,01015
Polymers45,0393
Non-polymers97212
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-48 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.786, 65.786, 237.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 31962.016 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide peptide from Tegument protein pp65


Mass: 1328.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Human herpesvirus 5 / References: UniProt: F5HB26, UniProt: Q6SW59*PLUS

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Non-polymers , 3 types, 470 molecules

#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 18% PEG2000-MME, 5-10mM NiCl2, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1
DetectorDate: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→25.281 Å / Num. all: 58565 / Num. obs: 56534 / % possible obs: 99.2 % / Redundancy: 11.9 % / Biso Wilson estimate: 27.79 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 37

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h6p

2h6p


Resolution: 1.7→25.281 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8701 / SU ML: 0.42 / σ(F): 1.33 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 2353 4.05 %RANDOM
Rwork0.1845 55713 --
obs0.1859 56534 99.21 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 102.1 Å2 / Biso mean: 35.476 Å2 / Biso min: 15.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 52 458 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183393
X-RAY DIFFRACTIONf_angle_d1.6994621
X-RAY DIFFRACTIONf_chiral_restr0.138467
X-RAY DIFFRACTIONf_plane_restr0.008615
X-RAY DIFFRACTIONf_dihedral_angle_d13.4541287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.76080.29962070.264655365743100
1.7608-1.83130.29312340.236554975731100
1.8313-1.91460.24782460.212654915737100
1.9146-2.01560.2232410.184855285769100
2.0156-2.14180.22352430.177655355778100
2.1418-2.3070.21922210.176755685789100
2.307-2.5390.22982510.183356025853100
2.539-2.9060.22252250.181656445869100
2.906-3.65940.20522420.16957035945100
3.6594-25.2840.20332430.18755609585293
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)
11.11620.4658-0.14022.56090.63241.91840.08040.0420.1362-0.0472-0.07050.2268-0.4686-0.3214-0.02350.27330.06660.02830.24470.00490.13667.4765-28.15-26.0382
21.2042-0.0247-0.07332.4420.73611.8957-0.030.26130.1123-0.27040.02190.0485-0.6701-0.3465-0.05980.33550.08790.03850.3180.03360.125310.1552-28.3617-35.9826
32.33021.24630.6472.6544-0.08681.7660.09290.0878-0.1608-0.09140.0145-0.5292-0.42510.2771-0.14170.2214-0.02710.06560.2921-0.02770.197920.1061-32.4434-27.9574
41.33350.9796-0.45351.5785-0.2442.12630.06370.2178-0.1712-0.25720.0474-0.549-0.41060.4527-0.07110.2527-0.06770.09340.3222-0.0450.264926.5874-31.9132-34.5754
50.58320.1364-0.47650.5434-0.02222.41350.10550.04350.1731-0.05290.0345-0.0093-0.43540.0255-0.05920.3328-0.04780.02510.0925-0.05220.130712.1268-26.194-2.2657
61.0313-0.202-0.5561.466-0.36913.339-0.0219-0.0877-0.07650.1865-0.0113-0.1675-0.06660.47570.03850.2633-0.06550.01540.2054-0.04950.136516.5483-33.82266.6115
71.75250.1256-0.07721.665-0.52041.5230.1713-0.2330.1480.3111-0.12630.07030.0233-0.39070.00750.1819-0.05720.01590.2679-0.04020.1462.2336-39.5649-10.2664
81.1581.1588-1.15842.7825-2.49795.6321-0.25470.98970.9269-0.51360.75921.46120.1908-1.3663-0.26350.2594-0.02870.01330.59760.00040.4164-8.753-38.2217-14.7017
90.938-0.1211.00492.3826-0.06521.07770.11-0.4360.07210.4489-0.0410.4486-0.0321-0.45360.2909-0.035-0.0458-0.04650.1339-0.0992-0.16021.9874-36.4395-11.7828
101.48850.27880.10742.14261.29482.53030.209-0.2968-0.17350.5434-0.136-0.05570.3996-0.3152-0.04030.2725-0.1088-0.01480.28280.01810.16711.2511-46.9014-7.9351
111.73750.56250.63310.18230.20510.2307-0.00510.3792-0.108-0.11820.2287-0.1774-0.29950.1310.3860.55420.02320.13180.40050.01410.255117.384-26.7947-37.5531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:52)A1 - 52
2X-RAY DIFFRACTION2(chain A and resid 53:85)A53 - 85
3X-RAY DIFFRACTION3(chain A and resid 86:116)A86 - 116
4X-RAY DIFFRACTION4(chain A and resid 117:165)A117 - 165
5X-RAY DIFFRACTION5(chain A and resid 166:212)A166 - 212
6X-RAY DIFFRACTION6(chain A and resid 213:275)A213 - 275
7X-RAY DIFFRACTION7(chain B and resid 1:43)B1 - 43
8X-RAY DIFFRACTION8(chain B and resid 44:51)B44 - 51
9X-RAY DIFFRACTION9(chain B and resid 52:78)B52 - 78
10X-RAY DIFFRACTION10(chain B and resid 79:99)B79 - 99
11X-RAY DIFFRACTION11(chain C and resid 1:11)C1 - 11

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