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- PDB-4may: Crystal structure of an immune complex -

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Basic information

Entry
Database: PDB / ID: 4may
TitleCrystal structure of an immune complex
Components
  • (MHC class II ...) x 2
  • HY.1B11 TCR alpha chain
  • UL15 peptide-HY.1B11 TCR beta chain, chimeric construct
KeywordsIMMUNE SYSTEM / immune complex / autoimmunity / multiple sclerosis / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / 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
MHC class II HLA-DQ-alpha chain / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified herpesvirus
homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSethi, D.K. / Wucherpfennig, K.W.
CitationJournal: Nat Commun / Year: 2013
Title: Crossreactivity of a human autoimmune TCR is dominated by a single TCR loop.
Authors: Sethi, D.K. / Gordo, S. / Schubert, D.A. / Wucherpfennig, K.W.
History
DepositionAug 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class II HLA-DQ-alpha chain
B: MHC class II antigen
C: HY.1B11 TCR alpha chain
D: UL15 peptide-HY.1B11 TCR beta chain, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7465
Polymers96,6504
Non-polymers961
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-86 kcal/mol
Surface area36900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.514, 123.176, 134.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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MHC class II ... , 2 types, 2 molecules AB

#1: Protein MHC class II HLA-DQ-alpha chain


Mass: 20762.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQ1 alpha chain, HLA-DQA1 / Plasmid: pEE13.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / References: UniProt: Q30066
#2: Protein MHC class II antigen


Mass: 23232.916 Da / Num. of mol.: 1 / Fragment: unp residues 31-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, HLA-DQ1 beta chain, HLA-DQB1
Plasmid: pEE13.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / References: UniProt: Q67AJ6

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Protein , 2 types, 2 molecules CD

#3: Protein HY.1B11 TCR alpha chain


Mass: 23266.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet22b / Production host: Escherichia coli (E. coli)
#4: Protein UL15 peptide-HY.1B11 TCR beta chain, chimeric construct


Mass: 29388.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified herpesvirus, homo sapiens / Plasmid: pet22b / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 356 molecules

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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE -21 TO -10 ARE PART OF PEPTIDE FROM UL15 PROTEIN OF HERPES VIRUS COVALENTLY ATTACHED TO ...RESIDUE -21 TO -10 ARE PART OF PEPTIDE FROM UL15 PROTEIN OF HERPES VIRUS COVALENTLY ATTACHED TO BETA CHAIN OF TCR THROUGH A LINKER

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 50mM Citrate buffer, 10% PEG8000,0.12M Ammonium Sulfate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 61669 / Num. obs: 61418 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 36.09 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.001 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.284.50.85760610.753199.7
2.28-2.374.60.69560110.724199.7
2.37-2.484.60.52961010.729199.8
2.48-2.614.60.38160910.741199.9
2.61-2.774.60.25461050.773199.9
2.77-2.994.60.15461550.8551100
2.99-3.294.60.0961380.9761100
3.29-3.764.60.05761871.2341100
3.76-4.744.50.0562281.931199.8
4.74-504.40.03563411.293197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.259 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8232 / SU ML: 0.25 / σ(F): 0 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 3127 5.1 %RANDOM
Rwork0.1963 ---
obs0.1984 61350 99.51 %-
all-61652 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.83 Å2 / Biso mean: 42.9739 Å2 / Biso min: 20.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6412 0 5 355 6772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086588
X-RAY DIFFRACTIONf_angle_d1.1918955
X-RAY DIFFRACTIONf_chiral_restr0.086970
X-RAY DIFFRACTIONf_plane_restr0.0041173
X-RAY DIFFRACTIONf_dihedral_angle_d14.3272365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2003-2.23470.26591490.25462526267597
2.2347-2.27130.29661400.255526262766100
2.2713-2.31040.33191380.25525782716100
2.3104-2.35250.34221420.243226492791100
2.3525-2.39770.3121360.248726182754100
2.3977-2.44660.29611460.23726052751100
2.4466-2.49980.26441270.233826712798100
2.4998-2.5580.2841510.229925882739100
2.558-2.62190.26761390.219126292768100
2.6219-2.69280.28071510.213326432794100
2.6928-2.7720.26031380.213326272765100
2.772-2.86150.31111490.219426362785100
2.8615-2.96370.23541480.215726322780100
2.9637-3.08230.28891300.208226772807100
3.0823-3.22250.22341220.213126812803100
3.2225-3.39230.26221470.198526602807100
3.3923-3.60470.23451400.19726682808100
3.6047-3.88280.21521470.182926732820100
3.8828-4.27320.20311460.162326892835100
4.2732-4.89050.16391580.142226772835100
4.8905-6.15770.1791360.1752713284999
6.1577-39.26560.23131470.19362757290496
Refinement TLS params.Method: refined / Origin x: -6.8254 Å / Origin y: 22.804 Å / Origin z: -30.2356 Å
111213212223313233
T0.2348 Å20.0011 Å20.0042 Å2-0.2286 Å2-0.003 Å2--0.2282 Å2
L0.2015 °2-0.1488 °20.2225 °2-0.3471 °2-0.3266 °2--0.4455 °2
S-0.0384 Å °-0.0561 Å °0.0179 Å °0.0953 Å °0.046 Å °0.0145 Å °-0.0801 Å °-0.1026 Å °0.0518 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 180
2X-RAY DIFFRACTION1allB3 - 191
3X-RAY DIFFRACTION1allC2 - 192
4X-RAY DIFFRACTION1allD-21 - 240
5X-RAY DIFFRACTION1all1
6X-RAY DIFFRACTION1allD - C1 - 397

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