PDB-8ew6: Anti-human CD8 VHH complex with CD8 alpha

ID or keywords:

Entry

Database: PDB / ID: 8ew6

Title

Anti-human CD8 VHH complex with CD8 alpha

Components

Anti-CD8 alpha VHH
T-cell surface glycoprotein CD8 alpha chain

Keywords

IMMUNE SYSTEM / CD8a / VHH / PET imaging

Function / homology

Function and homology information

cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity /

T cell receptor complex / plasma membrane raft / antigen processing and presentation / MHC class I protein binding /

coreceptor activity /

T cell activation /

cell surface receptor protein tyrosine kinase signaling pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.904 Å

Authors

Kiefer, J.R. / Williams, S. / Davies, C.W. / Koerber, J.T. / Sriraman, S.K. / Yin, Y.P.

Funding support

1items

Citation

Journal: Eur J Nucl Med Mol Imaging / Year: 2023
Title: Development of an 18 F-labeled anti-human CD8 VHH for same-day immunoPET imaging.
Authors: Sriraman, S.K. / Davies, C.W. / Gill, H. / Kiefer, J.R. / Yin, J. / Ogasawara, A. / Urrutia, A. / Javinal, V. / Lin, Z. / Seshasayee, D. / Abraham, R. / Haas, P. / Koth, C. / Marik, J. / ...

History

Deposition	Oct 21, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 1, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ew6.cif.gz	107.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8ew6.ent.gz	83.4 KB	Display	PDB format
PDBx/mmJSON format	8ew6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ew/8ew6 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/8ew6	HTTPS FTP

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Related structure data

Related structure data	7uvf
Similar structure data	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	#63 - Mar 2005 T-Cell Receptor similarity (2) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

W: T-cell surface glycoprotein CD8 alpha chain

V: Anti-CD8 alpha VHH

29.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

W: T-cell surface glycoprotein CD8 alpha chain

V: Anti-CD8 alpha VHH

W: T-cell surface glycoprotein CD8 alpha chain

V: Anti-CD8 alpha VHH

defined by author&software
Evidence: gel filtration
59.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.115, 83.554, 51.302
Angle α, β, γ (deg.)	90.000, 98.480, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	V-232- HOH

#1: Protein	T-cell surface glycoprotein CD8 alpha chain / T-lymphocyte differentiation antigen T8/Leu-2 Mass: 14563.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD8A, MAL / Production host: Escherichia coli (E. coli) / References: UniProt: P01732
#2: Antibody	Anti-CD8 alpha VHH Mass: 15018.536 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.05 Å³/Da / Density % sol: 39.89 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 15% PEG 3350 and 0.1M succinic acid pH 7.0

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Data collection

Diffraction

Mean temperature: 93 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1.00001 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.00001 Å / Relative weight: 1

Reflection

Resolution: 1.9→35 Å / Num. obs: 16891 / % possible obs: 90.9 % / Redundancy: 2.9 % / R_merge(I) obs: 0.048 / R_pim(I) all: 0.032 / R_rim(I) all: 0.058 / Χ²: 0.98 / Net I/σ(I): 11.4 / Num. measured all: 48809

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.93	2.4	0.254	636	0.869	0.186	0.316	0.584	69.5
1.93-1.97	2.4	0.235	659	0.912	0.17	0.292	0.606	69.8
1.97-2.01	2.5	0.215	697	0.929	0.154	0.266	0.608	77.4
2.01-2.05	2.5	0.193	720	0.947	0.14	0.24	0.653	77.9
2.05-2.09	2.4	0.166	752	0.948	0.123	0.208	0.667	80.4
2.09-2.14	2.6	0.158	786	0.964	0.113	0.196	0.668	85.2
2.14-2.19	2.7	0.129	827	0.974	0.089	0.157	0.643	88.5
2.19-2.25	2.9	0.125	822	0.977	0.084	0.152	0.768	89.8
2.25-2.32	2.9	0.115	859	0.98	0.078	0.139	0.689	91.7
2.32-2.39	2.8	0.1	880	0.985	0.068	0.122	0.719	95.2
2.39-2.48	2.7	0.092	895	0.986	0.064	0.113	0.76	96.7
2.48-2.58	2.8	0.088	907	0.987	0.06	0.107	0.834	98.2
2.58-2.7	2.9	0.069	911	0.992	0.047	0.084	0.81	98.7
2.7-2.84	3.2	0.061	933	0.995	0.039	0.073	0.91	99
2.84-3.02	3.2	0.055	915	0.995	0.035	0.065	1.041	99.5
3.02-3.25	3.1	0.05	930	0.995	0.033	0.06	1.246	99.7
3.25-3.57	3.2	0.046	937	0.996	0.03	0.055	1.47	100
3.57-4.09	3.4	0.042	930	0.997	0.027	0.05	1.48	99.8
4.09-5.15	3.2	0.038	939	0.995	0.026	0.046	1.448	99.8
5.15-35	3.3	0.041	956	0.994	0.027	0.049	1.518	99.9

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX	1.16_3549	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NULL

Resolution: 1.904→32.481 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 30.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2454	854	5.06 %
R_work	0.2002	16032	-
obs	0.2024	16886	90.43 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 103.15 Å² / B_iso mean: 43.9277 Å² / B_iso min: 19.67 Å²

Refinement step

Cycle: final / Resolution: 1.904→32.481 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1768	0	0	84	1852
B_iso mean	-	-	-	43.15	-
Num. residues	-	-	-	-	230

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.904-2.0233	0.3501	98	0.2639	2079	70
2.0233-2.1795	0.2661	128	0.2446	2411	83
2.1795-2.3988	0.3013	154	0.2506	2713	92
2.3988-2.7457	0.3022	163	0.2488	2873	98
2.7457-3.4587	0.2821	165	0.2116	2948	100
3.4587-32.48	0.19	146	0.1636	3008	100

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	1.5524	-1.1191	-0.6117	1.3628	-0.4928	1.6225	0.2625	-0.7336	0.463	0.2418	-0.3973	0.1741	-0.0185	-0.2743	-0.0027	0.3849	0.0797	0.075	0.4376	-0.057	0.3861	-49.1983	34.1292	23.4846
2	2.5117	0.2003	-0.145	1.3975	0.9112	2.1964	-0.0455	-0.2963	-0.0284	0.1672	-0.1563	0.251	0.2951	0.3218	-0.0001	0.3405	0.0613	0.0191	0.3591	0.0428	0.2205	-45.284	24.7041	19.8473
3	0.6082	0.1655	-0.4208	0.3757	0.3834	0.7229	0.418	0.2047	0.4343	-0.4755	-0.0698	0.1354	-0.1197	0.1354	0.0642	0.3871	0.0842	-0.0281	0.3777	0.0405	0.465	-42.4827	32.535	12.5399
4	1.3298	-0.4269	-0.3607	0.6947	0.9603	1.3828	0.1027	-0.3987	0.4758	0.11	0.2072	-0.4529	-0.1857	0.8479	0.0014	0.3005	-0.0118	-0.0717	0.5616	-0.0432	0.3308	-34.0367	29.1111	18.2136
5	3.2685	-0.5181	-0.4787	2.1803	1.4687	2.9363	-0.0322	-0.5307	0.2805	0.1933	0.0574	-0.0999	-0.038	0.2529	0.0003	0.2934	0.0315	-0.0575	0.3562	-0.0152	0.2328	-41.8137	30.2512	19.8915
6	2.3507	-0.2064	-0.2014	0.8535	0.5704	0.7726	0.2356	0.1641	0.4429	-0.4533	-0.1674	0.0961	-0.4327	-0.1062	0.0082	0.4834	0.0634	-0.0073	0.3334	0.0768	0.3633	-47.6059	30.723	13.4474
7	0.209	-0.2851	-0.306	0.8607	-0.1589	1.8856	-0.1008	-0.0893	-0.7385	0.9785	0.1037	-0.5394	0.0785	-0.013	0.001	0.5186	0.0816	0.0493	0.4658	0.1577	0.5423	-37.134	-1.1919	17.6563
8	0.0452	-0.0524	0.13	0.519	0.0781	0.33	-0.4465	0.2417	0.3301	-0.3016	0.1443	1.4158	0.0645	-0.3472	-0.0027	0.33	0.1158	0.0509	0.3906	0.097	0.4491	-37.8568	5.6611	13.6622
9	0.0805	0.1734	0.0257	0.2743	0.0157	0.0108	0.1323	0.1408	0.3169	-0.5326	-0.4449	0.3026	0.3127	0.6099	0.0014	0.4639	0.0824	-0.0345	0.4233	0.1147	0.2835	-30.7001	17.944	9.4978
10	0.4372	0.0117	0.4655	0.0284	0.0473	0.4226	-0.2053	-0.3343	-0.1968	-0.0233	0.3028	-0.3375	-0.1107	0.1916	0	0.4498	0.0625	0.2185	0.2658	0.0821	0.6757	-31.7098	0.572	6.5404
11	0.1602	0.0072	0.05	0.1065	-0.1078	0.1418	0.4656	-0.5036	-0.1544	-0.6989	-0.1811	-0.4535	0.3986	0.1783	0.0045	0.5355	-0.01	0.1865	0.3565	-0.0303	0.7604	-25.0796	-9.9108	6.6281
12	0.1867	0.1178	0.0841	0.0939	-0.0393	0.4478	0.1738	0.1357	-0.5683	-1.028	0.0025	-0.4302	-0.1227	-0.1297	-0.0001	0.3674	0.0193	0.1245	0.2127	0.0168	0.4436	-35.1206	4.3731	1.6522
13	0.7858	0.2264	0.8125	0.3811	-0.2676	1.5536	-0.1246	0.8813	-0.4567	-0.9915	-0.0433	0.9284	-0.3468	0.0926	0.0008	0.4486	0.0438	-0.0038	0.4208	-0.1101	0.6525	-43.1621	5.9196	4.5974
14	0.4207	-0.0868	-0.249	0.0512	0.1697	0.4403	-0.3162	-0.3006	-0.744	0.1225	0.1521	0.4705	0.1124	0.0532	-0.0096	0.341	0.0984	0.0275	0.2919	0.0835	0.4405	-40.6306	6.3258	10.2359
15	2.1202	-0.0229	-1.9466	0.1796	-0.2777	2.2957	-0.1548	1.3812	-0.3735	-0.9777	-0.6526	-0.286	2.0354	-0.1405	-0.3224	0.5889	0.0614	0.2456	0.3811	0.0936	0.7756	-39.4616	-12.1501	9.2503
16	0.655	0.6129	0.1994	0.5293	-0.0874	0.9932	-0.2361	0.2195	-0.8473	0.7451	0.3005	0.039	-0.4581	0.1183	0.0256	0.3059	0.0646	0.1122	0.3271	0.0807	0.628	-29.4204	3.2751	8.8837
17	1.483	1.7595	-0.5948	2.168	-0.6863	0.4251	-0.3416	0.3852	-0.7908	-0.7574	0.2753	-1.1842	-0.4076	0.1573	-0.0172	0.5438	0.0979	0.0188	0.4998	0.0723	0.498	-23.2583	12.3795	5.7551
18	4.0673	4.4951	-4.3902	5.5476	-4.1946	5.1063	0.4538	-1.6351	-0.2087	1.3128	-0.3911	0.5221	-0.4153	0.8292	0.3334	0.422	0.0522	0.0522	0.498	0.4369	0.7397	-31.8664	-6.3091	18.4

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'V' and (resid 1 through 17 )	V	1 - 17
2	X-RAY DIFFRACTION	2	chain 'V' and (resid 18 through 39 )	V	18 - 39
3	X-RAY DIFFRACTION	3	chain 'V' and (resid 40 through 52 )	V	40 - 52
4	X-RAY DIFFRACTION	4	chain 'V' and (resid 53 through 68 )	V	53 - 68
5	X-RAY DIFFRACTION	5	chain 'V' and (resid 69 through 105 )	V	69 - 105
6	X-RAY DIFFRACTION	6	chain 'V' and (resid 106 through 123 )	V	106 - 123
7	X-RAY DIFFRACTION	7	chain 'W' and (resid 1 through 17 )	W	1 - 17
8	X-RAY DIFFRACTION	8	chain 'W' and (resid 18 through 24 )	W	18 - 24
9	X-RAY DIFFRACTION	9	chain 'W' and (resid 25 through 31 )	W	25 - 31
10	X-RAY DIFFRACTION	10	chain 'W' and (resid 32 through 39 )	W	32 - 39
11	X-RAY DIFFRACTION	11	chain 'W' and (resid 40 through 46 )	W	40 - 46
12	X-RAY DIFFRACTION	12	chain 'W' and (resid 47 through 53 )	W	47 - 53
13	X-RAY DIFFRACTION	13	chain 'W' and (resid 54 through 73 )	W	54 - 73
14	X-RAY DIFFRACTION	14	chain 'W' and (resid 74 through 81 )	W	74 - 81
15	X-RAY DIFFRACTION	15	chain 'W' and (resid 82 through 89 )	W	82 - 89
16	X-RAY DIFFRACTION	16	chain 'W' and (resid 90 through 98 )	W	90 - 98
17	X-RAY DIFFRACTION	17	chain 'W' and (resid 99 through 104 )	W	99 - 104
18	X-RAY DIFFRACTION	18	chain 'W' and (resid 105 through 116 )	W	105 - 116

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