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- PDB-1r5v: Evidence that structural rearrangements and/or flexibility during... -

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Basic information

Entry
Database: PDB / ID: 1r5v
TitleEvidence that structural rearrangements and/or flexibility during TCR binding can contribute to T-cell activation
Components
  • H-2 class II histocompatibility antigen, E-K alpha chain
  • MHC H2-IE-beta
  • artificial peptide
KeywordsSIGNALING PROTEIN / TCR / MHC class II / structural rearangement
Function / homology
Function and homology information


response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosomal membrane
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 / MHC classes I/II-like antigen recognition protein ...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 / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, E-K alpha chain / H-2 class II histocompatibility antigen, I-A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKrogsgaard, M. / Prado, N. / Adams, E.J. / He, X.L. / Chow, D.C. / Wilson, D.B. / Garcia, K.C. / Davis, M.M.
CitationJournal: Mol.Cell / Year: 2003
Title: Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation.
Authors: Krogsgaard, M. / Prado, N. / Adams, E.J. / He, X.L. / Chow, D.C. / Wilson, D.B. / Garcia, K.C. / Davis, M.M.
History
DepositionOct 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: H-2 class II histocompatibility antigen, E-K alpha chain
E: artificial peptide
B: MHC H2-IE-beta
C: H-2 class II histocompatibility antigen, E-K alpha chain
F: artificial peptide
D: MHC H2-IE-beta


Theoretical massNumber of molelcules
Total (without water)88,2206
Polymers88,2206
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: H-2 class II histocompatibility antigen, E-K alpha chain
E: artificial peptide
B: MHC H2-IE-beta


Theoretical massNumber of molelcules
Total (without water)44,1103
Polymers44,1103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-36 kcal/mol
Surface area17800 Å2
MethodPISA
3
C: H-2 class II histocompatibility antigen, E-K alpha chain
F: artificial peptide
D: MHC H2-IE-beta


Theoretical massNumber of molelcules
Total (without water)44,1103
Polymers44,1103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-34 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.420, 104.650, 120.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H-2 class II histocompatibility antigen, E-K alpha chain


Mass: 20962.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEMEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLyss / References: UniProt: P04224
#2: Protein/peptide artificial peptide


Mass: 1410.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: artificial
#3: Protein MHC H2-IE-beta


Mass: 21737.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEMEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLyss / References: UniProt: P18468
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
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: 56.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMHEPES1droppH7.2
3150 mM1dropNaCl
40.9 Mcitrate1reservoir
50.1 Mcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 34039 / Num. obs: 34039 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.5
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.377 / % possible all: 75.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 144043
Reflection shell
*PLUS
% possible obs: 75.6 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 1700 RANDOM
Rwork0.213 --
all0.215 34039 -
obs0.215 34039 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.999 Å20 Å20 Å2
2---1.152 Å20 Å2
3---5.151 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 0 160 6288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.5→2.6 Å / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.284
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4ion.param
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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