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- PDB-2arj: CD8alpha-alpha in complex with YTS 105.18 Fab -

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Basic information

Entry
Database: PDB / ID: 2arj
TitleCD8alpha-alpha in complex with YTS 105.18 Fab
Components
  • T-cell surface glycoprotein CD8 alpha chain
  • YTS 105.18 antigen binding region Heavy chain
  • YTS 105.18 antigen binding region Light chain
KeywordsIMMUNE SYSTEM / Protein-protein complex / Antibody Fab / Immunoglobulin domain
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane raft / positive regulation of calcium-mediated signaling / T cell activation / T cell receptor signaling pathway / defense response to virus / adaptive immune response ...cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane raft / positive regulation of calcium-mediated signaling / T cell activation / T cell receptor signaling pathway / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / signaling receptor complex / external side of plasma membrane / protein kinase binding / cell surface / identical protein binding / plasma membrane
Similarity search - Function
CD8 alpha subunit / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...CD8 alpha subunit / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsShore, D.A. / Teyton, L. / Dwek, R.A. / Rudd, P.M. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of the TCR co-receptor CD8alphaalpha in complex with monoclonal antibody YTS 105.18 Fab fragment at 2.88 A resolution.
Authors: Shore, D.A. / Teyton, L. / Dwek, R.A. / Rudd, P.M. / Wilson, I.A.
History
DepositionAug 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: YTS 105.18 antigen binding region Light chain
H: YTS 105.18 antigen binding region Heavy chain
A: YTS 105.18 antigen binding region Light chain
B: YTS 105.18 antigen binding region Heavy chain
R: T-cell surface glycoprotein CD8 alpha chain
Q: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)120,6836
Polymers120,6836
Non-polymers00
Water21612
1
L: YTS 105.18 antigen binding region Light chain
H: YTS 105.18 antigen binding region Heavy chain
Q: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)60,3423
Polymers60,3423
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: YTS 105.18 antigen binding region Light chain
B: YTS 105.18 antigen binding region Heavy chain
R: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)60,3423
Polymers60,3423
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.344, 107.135, 131.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12L
22A
13B
23H
14B
24H
15R
25Q

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARG3LA1 - 1081 - 108
21ASPASPARGARG3AC1 - 1081 - 108
12ALAALAARGARG3LA109 - 211109 - 211
22ALAALAARGARG3AC109 - 211109 - 211
13GLNGLNTHRTHR3BD1 - 1101 - 114
23GLNGLNTHRTHR3HB1 - 1101 - 114
14ALAALAPROPRO3BD111 - 213115 - 202
24ALAALAPROPRO3HB111 - 213115 - 202
15ALAALAVALVAL2RE4 - 1224 - 122
25ALAALAVALVAL2QF4 - 1224 - 122

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Antibody YTS 105.18 antigen binding region Light chain


Mass: 23413.027 Da / Num. of mol.: 2 / Fragment: YTS 105.18 Fab Light Chain / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell line: Hybridoma / Strain: Y3 myeloma
#2: Antibody YTS 105.18 antigen binding region Heavy chain


Mass: 22971.666 Da / Num. of mol.: 2 / Fragment: YTS 105.18 Fab Heavy Chain / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell line: Hybridoma / Strain: Y3 myeloma / References: UniProt: Q5M839
#3: Protein T-cell surface glycoprotein CD8 alpha chain / T-cell surface glycoprotein Lyt-2


Mass: 13957.014 Da / Num. of mol.: 2 / Fragment: CD8alpha-alpha
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8a, Lyt-2, Lyt2 / Plasmid: pMT / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01731
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 299 K / Method: vapor diffusion / pH: 5.1
Details: 20% PEG 3,000, 0.1M Sodium Acetate, pH 5.1, VAPOR DIFFUSION, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2004 / Details: Direct coupling
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.88→49.629 Å / Num. all: 27040 / Num. obs: 26797 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 66.237 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 10.8
Reflection shellResolution: 2.884→3 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1775 / Num. unique all: 2532 / Rsym value: 0.69 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1ACY for YTS 105.18 Fab, PDB Entry: 1BQH for CD8 component

1acy

1bqh


Resolution: 2.88→49 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.862 / SU B: 41.04 / SU ML: 0.351 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27709 1346 5 %RANDOM
Rwork0.22041 ---
all0.22326 26749 --
obs0.22326 25403 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.869 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å20 Å20 Å2
2---2.91 Å20 Å2
3---0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.468 Å0.351 Å
Refinement stepCycle: LAST / Resolution: 2.88→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8322 0 0 12 8334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228532
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.94911623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76551067
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96324.435345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.978151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7681532
X-RAY DIFFRACTIONr_chiral_restr0.1150.21313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026422
X-RAY DIFFRACTIONr_nbd_refined0.2390.23639
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25735
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.21
X-RAY DIFFRACTIONr_mcbond_it1.35135448
X-RAY DIFFRACTIONr_mcangle_it258738
X-RAY DIFFRACTIONr_scbond_it4.14883523
X-RAY DIFFRACTIONr_scangle_it5.85112885
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L432tight positional0.070.05
2L412tight positional0.050.05
3B456tight positional0.040.05
4B392tight positional0.330.05
5R460tight positional0.110.05
5R457medium positional0.480.5
1L417loose positional0.445
2L386loose positional0.185
3B428loose positional0.335
4B317loose positional0.45
1L432tight thermal0.10.5
2L412tight thermal0.110.5
3B456tight thermal0.10.5
4B392tight thermal0.260.5
5R460tight thermal1.10.5
5R457medium thermal1.12
1L417loose thermal2.610
2L386loose thermal2.6710
3B428loose thermal2.6210
4B317loose thermal2.7310
LS refinement shellResolution: 2.884→2.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 87 -
Rwork0.351 1609 -
obs--85.79 %
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)
13.430.6726-1.41833.9135-1.35291.0740.0737-0.35950.33950.577-0.03850.2212-0.3257-0.1554-0.03510.11020.06370.02-0.1305-0.0606-0.167867.976449.990823.2239
22.2306-0.13810.92483.2516-0.59743.40610.00570.2036-0.2983-0.27690.00470.00320.41650.2398-0.0104-0.10790.03050.0068-0.1798-0.0715-0.197678.5715106.1082-18.4159
33.2942-1.10061.22213.7995-0.61532.49260.07890.010.19190.312-0.013-0.5181-0.04370.3122-0.0658-0.1359-0.0761-0.0339-0.1798-0.04-0.113386.288142.068913.2258
46.34750.62830.91592.0997-0.0033.8192-0.23990.4003-0.02860.20930.13710.09760.0128-0.05910.1028-0.22210.05460.0077-0.22510.0223-0.186670.354415.545616.8479
50.2918-0.4320.85112.80250.21453.48710.0614-0.0061-0.0050.2703-0.0675-0.36370.21120.51980.0061-0.21320.04580.0188-0.0877-0.0007-0.145587.9911114.12130.09
67.5263-1.30392.84613.5947-1.15974.82370.0837-0.35830.21170.10560.05540.3939-0.4054-0.6213-0.139-0.1357-0.07170.1215-0.0872-0.022-0.148674.6006139.8649-11.1085
72.69251.24940.4555.65780.37542.65070.0410.46380.4205-0.2946-0.0370.0578-0.29890.2308-0.004-0.14890.0187-0.0132-0.05820.0732-0.11677.3939143.1047-26.4721
81.8498-0.6172-0.54993.8946-1.00031.240.1057-0.24450.1010.21950.0425-0.2285-0.09530.0243-0.1482-0.13750.02340.0036-0.12210.04-0.208364.034613.424931.4629
93.253-1.043-0.21384.1276-0.26184.68440.19320.22150.25060.0497-0.10820.0613-0.2038-0.1113-0.0850.1584-0.0979-0.0262-0.14820.09210.138878.727766.8513-0.5026
103.44331.42710.04793.21730.39254.13260.1193-0.2114-0.13930.498-0.03780.44630.2626-0.3581-0.08150.34040.0260.0738-0.09510.06430.160576.257188.24317.1771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC1 - 1081 - 108
2X-RAY DIFFRACTION2LA1 - 1081 - 108
3X-RAY DIFFRACTION3BD1 - 1101 - 114
4X-RAY DIFFRACTION4BD111 - 213115 - 202
5X-RAY DIFFRACTION5HB1 - 1101 - 114
6X-RAY DIFFRACTION6HB111 - 213115 - 202
7X-RAY DIFFRACTION7LA109 - 211109 - 211
8X-RAY DIFFRACTION8AC109 - 211109 - 211
9X-RAY DIFFRACTION9RE4 - 1224 - 122
10X-RAY DIFFRACTION10QF4 - 1224 - 122

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