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

ID or keywords:

Entry

Database: PDB / ID: 2arj

Title

CD8alpha-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

Keywords

IMMUNE SYSTEM / Protein-protein complex / Antibody Fab / Immunoglobulin domain

Function / homology

Function and homology information

cytotoxic T cell differentiation / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of calcium-mediated signaling / T cell activation / calcium-mediated signaling / T cell receptor signaling pathway / defense response to virus / adaptive immune response / cell surface receptor signaling pathway ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.88 Å

Authors

Shore, D.A. / Teyton, L. / Dwek, R.A. / Rudd, P.M. / Wilson, I.A.

Citation

Journal: 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

Deposition	Aug 19, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2006	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 23, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2arj.cif.gz	215.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2arj_validation.pdf.gz	480 KB	Display	wwPDB validaton report
Full document	2arj_full_validation.pdf.gz	517.9 KB	Display
Data in XML	2arj_validation.xml.gz	40.2 KB	Display
Data in CIF	2arj_validation.cif.gz	55.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ar/2arj ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2arj	HTTPS FTP

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Related structure data

Related structure data	1acyS 1bqhS 1akj 1cd8 1nez 1q69 S: Starting model for refinement
Similar structure data	5tru-1 6p4b-2 5x8l-3 4bz2-d 6cbv-d 6j6y-1 6rp8-2 1x1b-2 5mo9-d 6p4a-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (2) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (2) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #182 - Feb 2015 Insulin receptor similarity (1)

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

121 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author
60.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author
60.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	L
2	1	A
1	2	L
2	2	A
1	3	B
2	3	H
1	4	B
2	4	H
1	5	R
2	5	Q

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	ARG	ARG	3	L	A	1 - 108	1 - 108
2	1	ASP	ASP	ARG	ARG	3	A	C	1 - 108	1 - 108
1	2	ALA	ALA	ARG	ARG	3	L	A	109 - 211	109 - 211
2	2	ALA	ALA	ARG	ARG	3	A	C	109 - 211	109 - 211
1	3	GLN	GLN	THR	THR	3	B	D	1 - 110	1 - 114
2	3	GLN	GLN	THR	THR	3	H	B	1 - 110	1 - 114
1	4	ALA	ALA	PRO	PRO	3	B	D	111 - 213	115 - 202
2	4	ALA	ALA	PRO	PRO	3	H	B	111 - 213	115 - 202
1	5	ALA	ALA	VAL	VAL	2	R	E	4 - 122	4 - 122
2	5	ALA	ALA	VAL	VAL	2	Q	F	4 - 122	4 - 122

NCS ensembles :

ID
1
2
3
4
5

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.2 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9796 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2004 / Details: Direct coupling
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 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 % / B_iso Wilson estimate: 66.237 Å² / R_merge(I) obs: 0.154 / R_sym value: 0.154 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.884→3 Å / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 1775 / Num. unique all: 2532 / R_sym value: 0.69 / % possible all: 95.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method 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. F_o:F_c: 0.914 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27709	1346	5 %	RANDOM
R_work	0.22041	-	-	-
all	0.22326	26749	-	-
obs	0.22326	25403	98.37 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.869 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.6 Å²	0 Å²	0 Å²
2-	-	-2.91 Å²	0 Å²
3-	-	-	0.31 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.468 Å	0.351 Å

Refinement step

Cycle: LAST / Resolution: 2.88→49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8322	0	0	12	8334

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	8532
X-RAY DIFFRACTION	r_angle_refined_deg	1.684	1.949	11623
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.765	5	1067
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.963	24.435	345
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.978	15	1369
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.768	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	1313
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6422
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	3639
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	5735
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	286
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.231	0.2	52
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.237	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.351	3	5448
X-RAY DIFFRACTION	r_mcangle_it	2	5	8738
X-RAY DIFFRACTION	r_scbond_it	4.148	8	3523
X-RAY DIFFRACTION	r_scangle_it	5.85	11	2885

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	L	432	tight positional	0.07	0.05
2	L	412	tight positional	0.05	0.05
3	B	456	tight positional	0.04	0.05
4	B	392	tight positional	0.33	0.05
5	R	460	tight positional	0.11	0.05
5	R	457	medium positional	0.48	0.5
1	L	417	loose positional	0.44	5
2	L	386	loose positional	0.18	5
3	B	428	loose positional	0.33	5
4	B	317	loose positional	0.4	5
1	L	432	tight thermal	0.1	0.5
2	L	412	tight thermal	0.11	0.5
3	B	456	tight thermal	0.1	0.5
4	B	392	tight thermal	0.26	0.5
5	R	460	tight thermal	1.1	0.5
5	R	457	medium thermal	1.1	2
1	L	417	loose thermal	2.6	10
2	L	386	loose thermal	2.67	10
3	B	428	loose thermal	2.62	10
4	B	317	loose thermal	2.73	10

LS refinement shell

Resolution: 2.884→2.959 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	87	-
R_work	0.351	1609	-
obs	-	-	85.79 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.43	0.6726	-1.4183	3.9135	-1.3529	1.074	0.0737	-0.3595	0.3395	0.577	-0.0385	0.2212	-0.3257	-0.1554	-0.0351	0.1102	0.0637	0.02	-0.1305	-0.0606	-0.1678	67.9764	49.9908	23.2239
2	2.2306	-0.1381	0.9248	3.2516	-0.5974	3.4061	0.0057	0.2036	-0.2983	-0.2769	0.0047	0.0032	0.4165	0.2398	-0.0104	-0.1079	0.0305	0.0068	-0.1798	-0.0715	-0.1976	78.5715	106.1082	-18.4159
3	3.2942	-1.1006	1.2221	3.7995	-0.6153	2.4926	0.0789	0.01	0.1919	0.312	-0.013	-0.5181	-0.0437	0.3122	-0.0658	-0.1359	-0.0761	-0.0339	-0.1798	-0.04	-0.1133	86.2881	42.0689	13.2258
4	6.3475	0.6283	0.9159	2.0997	-0.003	3.8192	-0.2399	0.4003	-0.0286	0.2093	0.1371	0.0976	0.0128	-0.0591	0.1028	-0.2221	0.0546	0.0077	-0.2251	0.0223	-0.1866	70.3544	15.5456	16.8479
5	0.2918	-0.432	0.8511	2.8025	0.2145	3.4871	0.0614	-0.0061	-0.005	0.2703	-0.0675	-0.3637	0.2112	0.5198	0.0061	-0.2132	0.0458	0.0188	-0.0877	-0.0007	-0.1455	87.9911	114.1213	0.09
6	7.5263	-1.3039	2.8461	3.5947	-1.1597	4.8237	0.0837	-0.3583	0.2117	0.1056	0.0554	0.3939	-0.4054	-0.6213	-0.139	-0.1357	-0.0717	0.1215	-0.0872	-0.022	-0.1486	74.6006	139.8649	-11.1085
7	2.6925	1.2494	0.455	5.6578	0.3754	2.6507	0.041	0.4638	0.4205	-0.2946	-0.037	0.0578	-0.2989	0.2308	-0.004	-0.1489	0.0187	-0.0132	-0.0582	0.0732	-0.116	77.3939	143.1047	-26.4721
8	1.8498	-0.6172	-0.5499	3.8946	-1.0003	1.24	0.1057	-0.2445	0.101	0.2195	0.0425	-0.2285	-0.0953	0.0243	-0.1482	-0.1375	0.0234	0.0036	-0.1221	0.04	-0.2083	64.0346	13.4249	31.4629
9	3.253	-1.043	-0.2138	4.1276	-0.2618	4.6844	0.1932	0.2215	0.2506	0.0497	-0.1082	0.0613	-0.2038	-0.1113	-0.085	0.1584	-0.0979	-0.0262	-0.1482	0.0921	0.1388	78.7277	66.8513	-0.5026
10	3.4433	1.4271	0.0479	3.2173	0.3925	4.1326	0.1193	-0.2114	-0.1393	0.498	-0.0378	0.4463	0.2626	-0.3581	-0.0815	0.3404	0.026	0.0738	-0.0951	0.0643	0.1605	76.2571	88.2431	7.1771

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	C	1 - 108	1 - 108
2	X-RAY DIFFRACTION	2	L	A	1 - 108	1 - 108
3	X-RAY DIFFRACTION	3	B	D	1 - 110	1 - 114
4	X-RAY DIFFRACTION	4	B	D	111 - 213	115 - 202
5	X-RAY DIFFRACTION	5	H	B	1 - 110	1 - 114
6	X-RAY DIFFRACTION	6	H	B	111 - 213	115 - 202
7	X-RAY DIFFRACTION	7	L	A	109 - 211	109 - 211
8	X-RAY DIFFRACTION	8	A	C	109 - 211	109 - 211
9	X-RAY DIFFRACTION	9	R	E	4 - 122	4 - 122
10	X-RAY DIFFRACTION	10	Q	F	4 - 122	4 - 122

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