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- PDB-3tf7: 42F3 QL9/H2-Ld complex -

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Basic information

Entry
Database: PDB / ID: 3tf7
Title42F3 QL9/H2-Ld complex
Components
  • 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)
  • H2-Ld SBM2
  • QL9 peptide (QLSPFPFDL)
KeywordsIMMUNE SYSTEM / Ig and MHC / Antigen Recognition / TCR-pMHC / Membrane Receptors
Function / homology
Function and homology information


OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / : / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / succinyl-CoA metabolic process / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / oxoglutarate dehydrogenase complex ...OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / : / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / succinyl-CoA metabolic process / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / oxoglutarate dehydrogenase complex / pyramidal neuron development / thalamus development / striatum development / 2-oxoglutarate metabolic process / Mitochondrial protein degradation / thiamine pyrophosphate binding / antigen processing and presentation of peptide antigen via MHC class I / hippocampus development / generation of precursor metabolites and energy / glycolytic process / lumenal side of endoplasmic reticulum membrane / mitochondrial membrane / defense response / MHC class I protein complex / phagocytic vesicle membrane / immune response / mitochondrion / metal ion binding / nucleus
Similarity search - Function
2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate-binding fold / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, L-D alpha chain / 2-oxoglutarate dehydrogenase complex component E1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: H2-Ld SBM2
F: QL9 peptide (QLSPFPFDL)
C: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)
A: H2-Ld SBM2
B: QL9 peptide (QLSPFPFDL)
G: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)
I: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)
K: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,43210
Polymers154,2488
Non-polymers1842
Water00
1
C: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)
A: H2-Ld SBM2
B: QL9 peptide (QLSPFPFDL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7224
Polymers49,6303
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area9860 Å2
2
E: H2-Ld SBM2
F: QL9 peptide (QLSPFPFDL)
G: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7224
Polymers49,6303
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-5 kcal/mol
Surface area21420 Å2
3
I: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)


Theoretical massNumber of molelcules
Total (without water)27,4941
Polymers27,4941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: 42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)


Theoretical massNumber of molelcules
Total (without water)27,4941
Polymers27,4941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.487, 109.793, 213.590
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 H2-Ld SBM2


Mass: 21072.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01897*PLUS
#2: Protein/peptide QL9 peptide (QLSPFPFDL)


Mass: 1063.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Anaspec / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q60597*PLUS
#3: Protein
42F3 Mut7 scFv (42F3 alpha chain, linker, 42F3 beta chain)


Mass: 27494.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
Has protein modificationY
Sequence detailsTHE 42F3 PROTEIN (CHAIN C,G I AND K) IS A SINGLE CHAIN FV FRAGMENT OF THE THE 42F3 ALPHA BETA TCR. ...THE 42F3 PROTEIN (CHAIN C,G I AND K) IS A SINGLE CHAIN FV FRAGMENT OF THE THE 42F3 ALPHA BETA TCR. THE FV FRAGMENT IS DERIVED FROM TWO PROTEIN CHAINS (ALPHA AND BETA) AND FUSED TOGETHER WITH AN UNNATURAL LINKER SEQUENCE (GGGGSGGGGSGGGGSGGGGS). RESIDUES 1-113 CORRESPOND TO THE ALPHA CHAIN, RESIDUES 134-147 CORRESPOND TO THE BETA CHAIN) AND RESIDUES 248-253 CORRESPOND TO THE C-TERMINAL EXPRESSION TAG.

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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: 3.9 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 298 K / pH: 8.25
Details: 7% (w/v) PEG 17500, 100mM Bicine pH 8.25. 30% Glycerol cryo addiditive, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 61762 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.049
Reflection shellResolution: 2.75→2.85 Å / % possible all: 89.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OI9

2oi9


Resolution: 2.75→37.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 27.259 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3124 5.1 %RANDOM
Rwork0.237 ---
obs0.238 58631 97 %-
all-61755 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.75→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10126 0 12 0 10138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02110441
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.93914154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6751264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88823.212520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.818151628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.961574
X-RAY DIFFRACTIONr_chiral_restr0.0660.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218160
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.321.56316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.522210109
X-RAY DIFFRACTIONr_scbond_it0.49434125
X-RAY DIFFRACTIONr_scangle_it0.8654.54045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 229 -
Rwork0.365 3801 -
obs--87.38 %
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)
13.76380.5624-1.48435.5961-0.88115.0094-0.34640.0141-0.58070.1156-0.4282-0.65640.59710.49930.7747-0.27630.09210-0.07790.06260.045514.466-2.195-21.424
21.99590.2277-2.95181.15112.259310.3557-0.08340.1474-0.1045-0.2108-0.1088-0.61710.88330.18310.1922-0.1430.008-0.06440.1414-0.01540.12967.1870.194-19.85
33.2986-0.30490.12715.10410.62124.6342-0.23390.3964-0.0442-0.6824-0.0656-0.0197-0.4720.18880.2996-0.0061-0.1646-0.0382-0.0222-0.063-0.2743-30.32-16.195-47.342
41.04870.0334-0.03368.20951.88811.4558-0.13-0.15970.00330.2311-0.02080.38850.0877-0.06010.1509-0.1489-0.03510.01960.0044-0.0562-0.1124-34.448-12.032-24.27
56.19050.5371-0.19915.0525-1.3963.5647-0.16130.1989-0.6562-0.4545-0.2399-0.79480.52260.65060.4013-0.11580.07680.1739-0.15480.00290.1245-22.242-43.498-31.766
60.0167-0.0705-0.45410.29681.91212.31690.5574-0.5583-0.41040.054-0.2897-0.0757-0.06190.6364-0.26760.03510.01660.0824-0.03530.00650.1826-24.917-36.172-33.092
75.2476-0.33080.08372.27760.63465.10130.2846-0.4704-0.19870.3691-0.21360.17160.3671-0.6274-0.071-0.0595-0.1758-0.05310.0219-0.0806-0.1926-12.0615.258-4.705
87.4780.61681.88583.27-0.44062.43990.02720.26530.4217-0.324-0.01460.0814-0.0288-0.0621-0.0126-0.0854-0.0224-0.0685-0.0419-0.033-0.2137-15.8758.26-27.337
94.30060.68490.83727.9475-0.66823.9113-0.0234-0.2920.01160.707-0.0067-0.4539-0.0671-0.1470.03020.0958-0.0095-0.1432-0.135-0.0515-0.287110.6097.77917.088
101.17922.30220.66710.72184.51832.0383-0.06670.0060.5413-0.4103-0.33991.1486-0.0729-0.12690.40660.0928-0.0046-0.1024-0.075-0.08270.06234.44630.50310.477
115.2451-1.0789-0.81169.97943.8326.30040.080.4394-0.5901-0.5765-0.86981.3287-0.3758-0.40780.7898-0.1139-0.0055-0.12770.246-0.30610.0994-32.452-38.264-70.361
129.6721.20066.50115.64280.90995.8579-0.08280.1392-0.4448-0.2328-0.27311.56420.2736-0.80260.35590.174-0.04620.01910.6437-0.52160.7668-53.317-30.676-63.298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E2 - 175
2X-RAY DIFFRACTION2F1 - 9
3X-RAY DIFFRACTION3C1 - 113
4X-RAY DIFFRACTION4C135 - 253
5X-RAY DIFFRACTION5A1 - 175
6X-RAY DIFFRACTION6B1 - 9
7X-RAY DIFFRACTION7G1 - 112
8X-RAY DIFFRACTION8G136 - 247
9X-RAY DIFFRACTION9I2 - 112
10X-RAY DIFFRACTION10I135 - 251
11X-RAY DIFFRACTION11K1 - 113
12X-RAY DIFFRACTION12K136 - 246

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