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- PDB-3tpu: 42F3 p5E8/H2-Ld complex -

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Basic information

Entry
Database: PDB / ID: 3tpu
Title42F3 p5E8/H2-Ld complex
Components
  • 42F3 alpha
  • 42F3 beta
  • H2-Ld SBM2
  • p5E8 peptide
KeywordsIMMUNE SYSTEM / IG MHC / Antigen Recognition / TCR-pMHC / chimera protein / Membrane Receptor
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / integral component of lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / phagocytic vesicle membrane / immune response / external side of plasma membrane / extracellular space
Similarity search - Function
MHC_I C-terminus / MHC class I, alpha chain, C-terminal / MHC class I alpha chain, alpha1 alpha2 domains / MHC class I-like antigen recognition-like / Class I Histocompatibility antigen, domains alpha 1 and 2 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC_I C-terminus / MHC class I, alpha chain, C-terminal / MHC class I alpha chain, alpha1 alpha2 domains / MHC class I-like antigen recognition-like / Class I Histocompatibility antigen, domains alpha 1 and 2 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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
H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAdams, J.J. / Kranz, D.M. / Garcia, K.C.
CitationJournal: Immunity / Year: 2011
Title: T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex.
Authors: Adams, J.J. / Narayanan, S. / Liu, B. / Birnbaum, M.E. / Kruse, A.C. / Bowerman, N.A. / Chen, W. / Levin, A.M. / Connolly, J.M. / Zhu, C. / Kranz, D.M. / Garcia, K.C.
History
DepositionSep 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 42F3 alpha
B: 42F3 beta
I: H2-Ld SBM2
J: p5E8 peptide
C: 42F3 alpha
D: 42F3 beta
E: H2-Ld SBM2
F: p5E8 peptide
G: 42F3 alpha
H: 42F3 beta
K: H2-Ld SBM2
L: p5E8 peptide
M: 42F3 alpha
N: 42F3 beta
Q: H2-Ld SBM2
R: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,77832
Polymers291,27516
Non-polymers1,50316
Water724
1
A: 42F3 alpha
B: 42F3 beta
I: H2-Ld SBM2
J: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2038
Polymers72,8194
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 42F3 alpha
D: 42F3 beta
E: H2-Ld SBM2
F: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1077
Polymers72,8194
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 42F3 alpha
H: 42F3 beta
K: H2-Ld SBM2
L: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2999
Polymers72,8194
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: 42F3 alpha
N: 42F3 beta
Q: H2-Ld SBM2
R: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1698
Polymers72,8194
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)291.332, 291.332, 291.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11K-181-

SO4

21N-242-

SO4

31N-242-

SO4

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Components

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Protein , 3 types, 12 molecules ACGMBDHNIEKQ

#1: Protein
42F3 alpha


Mass: 23326.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
#2: Protein
42F3 beta


Mass: 27248.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
#3: Protein
H2-Ld SBM2


Mass: 21072.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P01897*PLUS

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Protein/peptide , 1 types, 4 molecules JFLR

#4: Protein/peptide
p5E8 peptide


Mass: 1171.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: GenScript

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Non-polymers , 3 types, 20 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.4
Details: 1.1M lithium sulfate, 1% (v/v) PEG 200 and 0.1M sodium acetate pH 4.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 21, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→84.07 Å / Num. all: 104323 / Num. obs: 104323 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3.06 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TFK
Resolution: 3.1→45.313 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 4271 5.01 %random
Rwork0.2309 ---
all0.2322 85599 --
obs0.2322 85334 99.69 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.394 Å2 / ksol: 0.305 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.8366 Å2-0 Å20 Å2
2---7.8366 Å2-0 Å2
3---26.1993 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20065 0 79 4 20148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01520684
X-RAY DIFFRACTIONf_angle_d1.55528074
X-RAY DIFFRACTIONf_dihedral_angle_d17.0387391
X-RAY DIFFRACTIONf_chiral_restr0.0932892
X-RAY DIFFRACTIONf_plane_restr0.0093669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.13530.35591570.34412580X-RAY DIFFRACTION96
3.1353-3.17210.33641460.31662625X-RAY DIFFRACTION98
3.1721-3.21080.28241300.31022664X-RAY DIFFRACTION99
3.2108-3.25150.33991360.30032662X-RAY DIFFRACTION100
3.2515-3.29420.31641390.29792714X-RAY DIFFRACTION100
3.2942-3.33930.35451320.29652663X-RAY DIFFRACTION100
3.3393-3.3870.33111530.28762683X-RAY DIFFRACTION100
3.387-3.43760.35191210.27922695X-RAY DIFFRACTION100
3.4376-3.49130.3331460.282698X-RAY DIFFRACTION100
3.4913-3.54850.30651510.272698X-RAY DIFFRACTION100
3.5485-3.60960.29531350.27852726X-RAY DIFFRACTION100
3.6096-3.67530.2861440.26032681X-RAY DIFFRACTION100
3.6753-3.74590.29131460.25132705X-RAY DIFFRACTION100
3.7459-3.82230.28821380.24542684X-RAY DIFFRACTION100
3.8223-3.90540.29671400.22942692X-RAY DIFFRACTION100
3.9054-3.99620.26151280.22222730X-RAY DIFFRACTION100
3.9962-4.09610.27171510.21512672X-RAY DIFFRACTION100
4.0961-4.20670.22211320.20382740X-RAY DIFFRACTION100
4.2067-4.33040.20371390.19192704X-RAY DIFFRACTION100
4.3304-4.47010.20931410.18932694X-RAY DIFFRACTION100
4.4701-4.62970.19171480.17052730X-RAY DIFFRACTION100
4.6297-4.81490.19341380.18132685X-RAY DIFFRACTION100
4.8149-5.03370.22871480.20432727X-RAY DIFFRACTION100
5.0337-5.29880.24851250.20882738X-RAY DIFFRACTION100
5.2988-5.63020.26251360.21772722X-RAY DIFFRACTION100
5.6302-6.06390.23151520.21372728X-RAY DIFFRACTION100
6.0639-6.67250.23431490.22072728X-RAY DIFFRACTION100
6.6725-7.6340.24581460.20422730X-RAY DIFFRACTION100
7.634-9.6030.20551670.19072750X-RAY DIFFRACTION100
9.603-45.3180.27051570.2642815X-RAY DIFFRACTION99

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