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- PDB-3q5y: V beta/V beta homodimerization-based pre-TCR model suggested by T... -

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Basic information

Entry
Database: PDB / ID: 3q5y
TitleV beta/V beta homodimerization-based pre-TCR model suggested by TCR beta crystal structures
ComponentsTCR N15 beta
KeywordsIMMUNE SYSTEM / IG / T cell receptor / antigen peptide/MHC / membrane
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, Q. / Zhang, H. / Wang, J.-H.
CitationJournal: Front Immunol / Year: 2011
Title: A conserved hydrophobic patch on Vbeta domains revealed by TCRbeta chain crystal structures: implications for pre-TCR dimerization
Authors: Zhou, B. / Chen, Q. / Mallis, R.J. / Zhang, H. / Liu, J.H. / Reinherz, E.L. / Wang, J.H.
History
DepositionDec 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 15, 2014Group: Structure summary
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: TCR N15 beta
B: TCR N15 beta
C: TCR N15 beta
D: TCR N15 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,94414
Polymers109,7034
Non-polymers1,24110
Water16,916939
1
A: TCR N15 beta
B: TCR N15 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4867
Polymers54,8512
Non-polymers6355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: TCR N15 beta
D: TCR N15 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4587
Polymers54,8512
Non-polymers6075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.182, 129.561, 129.702
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
TCR N15 beta


Mass: 27425.729 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-11d / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % PEG 3350, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9794 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 98361 / Num. obs: 97771 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.8 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.93 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21777 5151 5 %RANDOM
Rwork0.17825 ---
all0.1816 98361 --
obs0.18022 -99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7696 0 80 939 8715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218049
X-RAY DIFFRACTIONr_bond_other_d00.026957
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.93910904
X-RAY DIFFRACTIONr_angle_other_deg0.596316288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90623.75400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.934151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2621553
X-RAY DIFFRACTIONr_chiral_restr0.0740.21111
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218937
X-RAY DIFFRACTIONr_gen_planes_other00.021700
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.54790
X-RAY DIFFRACTIONr_mcbond_other0.1421.51935
X-RAY DIFFRACTIONr_mcangle_it1.20327745
X-RAY DIFFRACTIONr_scbond_it1.87633259
X-RAY DIFFRACTIONr_scangle_it3.0544.53152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 319 -
Rwork0.225 6742 -
obs--93.73 %
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)
11.2884-0.2062-0.11961.7964-0.03324.81750.0615-0.01680.1049-0.103-0.0462-0.142-0.19190.2185-0.01530.03120.00810.02360.0308-0.00620.08729.152-40.28513.381
24.65171.2821-1.01121.2898-0.09461.54580.0191-0.10450.01760.03270.0222-0.01970.02340.0595-0.04130.05050.0061-0.00430.0140.00740.014810.57-49.73737.718
32.0948-0.1994-0.85511.6572-0.25484.19350.0705-0.0125-0.1597-0.1733-0.06680.20450.2134-0.1678-0.00370.05030.0063-0.04570.019-0.00460.12358.768-28.37514.527
44.32131.36490.43761.8737-0.03542.0656-0.01810.05070.02830.1053-0.01790.028-0.0191-0.07650.0360.0344-0.0050.00140.0105-0.00840.009727.27-18.54539.108
51.75880.56740.0393.97580.39531.85020.00980.148-0.031-0.19750.03960.1026-0.0898-0.1633-0.04940.02560.02110.010.11-0.00290.0279-9.37917.7986.975
64.5356-0.58731.66551.8954-0.17082.13790.0336-0.1008-0.03390.00120.0120.10730.1048-0.1065-0.04560.0238-0.0121-0.00370.01080.00890.02078.377-7.5215.909
71.7105-0.1771-0.19554.1790.11172.07070.0878-0.0916-0.02590.2205-0.0228-0.1985-0.14490.243-0.0650.0387-0.04560.00530.1102-0.01180.037211.15719.006-4.881
84.84880.93221.35931.86240.02071.6893-0.0040.0413-0.0246-0.04020.0164-0.06880.04680.0345-0.01230.042-0.0070.00340.0099-0.01430.0251-8.056-4.189-15.288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 114
2X-RAY DIFFRACTION2A115 - 240
3X-RAY DIFFRACTION3B2 - 115
4X-RAY DIFFRACTION4B116 - 239
5X-RAY DIFFRACTION5C2 - 115
6X-RAY DIFFRACTION6C116 - 240
7X-RAY DIFFRACTION7D2 - 114
8X-RAY DIFFRACTION8D115 - 239

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