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- PDB-3ioz: SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93) -

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Basic information

Entry
Database: PDB / ID: 3ioz
TitleSIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)
Components
  • Protein Nef
  • T-cell surface glycoprotein CD3 zeta chain
KeywordsVIRAL PROTEIN/SIGNALING PROTEIN / Protein-Protein complex / Cell membrane / Lipoprotein / Membrane / Myristate / Viral immunoevasion / Virulence / Disulfide bond / Host-virus interaction / Phosphoprotein / Receptor / Transmembrane / VIRAL PROTEIN-ANTIVIRAL PROTEIN COMPLEX / VIRAL PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


gamma-delta T cell receptor complex / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface / Nef and signal transduction / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains ...gamma-delta T cell receptor complex / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface / Nef and signal transduction / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / FCGR activation / PD-1 signaling / Role of phospholipids in phagocytosis / FCGR3A-mediated IL10 synthesis / protein tyrosine kinase binding / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / protein complex oligomerization / T cell receptor signaling pathway / protein-containing complex assembly / adaptive immune response / receptor-mediated endocytosis of virus by host cell / cell surface receptor signaling pathway / protein heterodimerization activity / virus-mediated perturbation of host defense response / GTP binding / Golgi apparatus / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / HIV negative factor Nef ...Nef Regulatory Factor / Nef Regulatory Factor / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 zeta chain / Protein Nef
Similarity search - Component
Biological speciesSimian immunodeficiency virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.699 Å
AuthorsKim, W.M. / Sigalov, A.B. / Stern, L.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.
Authors: Kim, W.M. / Sigalov, A.B. / Stern, L.J.
History
DepositionAug 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Protein Nef
B: T-cell surface glycoprotein CD3 zeta chain


Theoretical massNumber of molelcules
Total (without water)21,9782
Polymers21,9782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-6 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.638, 51.638, 189.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein Nef


Mass: 16698.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5QGG3
#2: Protein/peptide T-cell surface glycoprotein CD3 zeta chain / T-cell receptor T3 zeta chain


Mass: 5279.782 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P20963

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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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 15% PEG 3350, 0.15M KF, 0.1M hepes, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 3122 / % possible obs: 99.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.051 / Χ2: 1.037 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.7-3.8312.70.3932821.0371100
3.83-3.9913.10.2793111.0071100
3.99-4.1713.40.1692931.0571100
4.17-4.3913.30.1583061.021100
4.39-4.6613.10.1013051.0571100
4.66-5.0213.20.093051.0611100
5.02-5.5312.70.0723111.0511100
5.53-6.3212.50.0563170.986199.7
6.32-7.96120.0393250.9981100
7.96-5010.80.033671.098195.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.53 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5 Å28.92 Å
Translation5 Å28.92 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.699→35.854 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.577 / SU ML: 2.17 / σ(F): 0.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.329 128 4.38 %
Rwork0.301 --
obs0.302 2923 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 143.65 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 251.08 Å2 / Biso mean: 206.485 Å2 / Biso min: 162.98 Å2
Baniso -1Baniso -2Baniso -3
1-28.379 Å20 Å2-0 Å2
2--28.379 Å20 Å2
3----84.592 Å2
Refinement stepCycle: LAST / Resolution: 3.699→35.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 0 0 1051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031088
X-RAY DIFFRACTIONf_angle_d0.5651478
X-RAY DIFFRACTIONf_chiral_restr0.04144
X-RAY DIFFRACTIONf_plane_restr0.003187
X-RAY DIFFRACTIONf_dihedral_angle_d13.315383
LS refinement shellHighest resolution: 3.699 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.329 128 -
Rwork0.301 2795 -
all-2923 -
obs--94 %

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