PDB-8gy5: High-resolution structure of the cemiplimab Fab in complex with PD-1

ID or keywords:

Entry

Database: PDB / ID: 8gy5

Title

High-resolution structure of the cemiplimab Fab in complex with PD-1

Components

Programmed cell death protein 1
heavy chain
light chain

Keywords

IMMUNE SYSTEM / cemiplimab / PD-1 / antibody

Function / homology

Function and homology information

negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / adaptive immune response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Heo, Y.-S. / Jeong, T.J.

Funding support

Korea, Republic Of, 1items

Citation

Journal: To Be Published
Title: High-resolution structure of the cemiplimab Fab in complex with PD-1
Authors: Heo, Y.-S. / Jeong, T.J.

History

Deposition	Sep 21, 2022	Deposition site: PDBJ / Processing site: PDBE
Revision 1.0	Oct 4, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gy5.cif.gz	435.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8gy5.ent.gz	357.1 KB	Display	PDB format
PDBx/mmJSON format	8gy5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gy5_validation.pdf.gz	471.8 KB	Display	wwPDB validaton report
Full document	8gy5_full_validation.pdf.gz	483.7 KB	Display
Data in XML	8gy5_validation.xml.gz	45.6 KB	Display
Data in CIF	8gy5_validation.cif.gz	66 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gy/8gy5 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/8gy5	HTTPS FTP

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Related structure data

Related structure data	5ggsS S: Starting model for refinement
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	#204 - Dec 2016 PD-1 similarity (4) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#204 - Dec 2016
PD-1
similarity (4)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#247 - Jul 2020
Myelin-associated Glycoprotein
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)

Deposited unit

A: heavy chain

B: light chain

Q: Programmed cell death protein 1

H: heavy chain

L: light chain

P: Programmed cell death protein 1

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

1

A: heavy chain

B: light chain

Q: Programmed cell death protein 1

defined by author
Evidence: gel filtration
61.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: heavy chain

L: light chain

P: Programmed cell death protein 1

defined by author
Evidence: gel filtration
61.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.060, 62.960, 81.290
Angle α, β, γ (deg.)	105.730, 98.000, 92.440
Int Tables number	1
Space group name H-M	P1

#1: Antibody	heavy chain Mass: 24493.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	light chain Mass: 23274.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein	Programmed cell death protein 1 / Protein PD-1 / hPD-1 Mass: 14083.601 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.16 Å³/Da / Density % sol: 43.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.98→30 Å / Num. obs: 71456 / % possible obs: 94.5 % / Redundancy: 2.8 % / B_iso Wilson estimate: 30.46 Å² / CC_1/2: 0.998 / Net I/σ(I): 10.9
Reflection shell	Resolution: 1.98→2.05 Å / Num. unique obs: 3596 / CC_1/2: 0.76

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Processing

Software

Name	Version	Classification
XDS		data scaling
PHENIX	1.20_4459	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ggs

5ggs

Resolution: 1.98→29.61 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2355	3418	5 %
R_work	0.187	64968	-
obs	0.1894	68386	94.71 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 101.08 Å² / B_iso mean: 38.297 Å² / B_iso min: 20.47 Å²

Refinement step

Cycle: final / Resolution: 1.98→29.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8210	0	0	644	8854
B_iso mean	-	-	-	41.61	-
Num. residues	-	-	-	-	1074

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.98-2.01	0.3109	143	0.2768	2713	2856	95
2.01-2.04	0.3443	142	0.2742	2712	2854	94
2.04-2.07	0.2831	142	0.2649	2682	2824	96
2.07-2.1	0.2846	145	0.2466	2765	2910	95
2.1-2.14	0.3109	144	0.2304	2738	2882	95
2.14-2.18	0.2794	144	0.2431	2727	2871	95
2.18-2.22	0.3161	141	0.2289	2675	2816	94
2.22-2.27	0.2797	145	0.2273	2762	2907	96
2.27-2.32	0.3096	143	0.2271	2706	2849	94
2.32-2.37	0.2702	141	0.2075	2687	2828	95
2.37-2.43	0.2291	142	0.216	2690	2832	95
2.43-2.49	0.2736	143	0.2061	2717	2860	94
2.49-2.57	0.248	138	0.2017	2631	2769	94
2.57-2.65	0.2504	140	0.2054	2655	2795	91
2.65-2.75	0.2575	138	0.2017	2619	2757	91
2.75-2.86	0.2182	144	0.1871	2742	2886	97
2.86-2.98	0.2326	145	0.2003	2738	2883	96
2.98-3.14	0.2615	144	0.1924	2753	2897	96
3.14-3.34	0.2178	144	0.1826	2728	2872	96
3.34-3.6	0.2387	144	0.1699	2734	2878	95
3.6-3.96	0.2144	144	0.167	2731	2875	95
3.96-4.53	0.1882	142	0.1405	2694	2836	94
4.53-5.7	0.1869	136	0.1448	2591	2727	91
5.7-29.61	0.1986	144	0.1742	2778	2922	97

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	5.1672	0.2106	-1.0917	0.6808	-0.3009	2.2667	-0.0346	-0.6695	0.0968	0.2106	-0.0282	-0.045	-0.0367	0.1564	0.0582	0.2452	0.0308	-0.046	0.254	-0.0205	0.2151	44.5055	5.5193	63.5792
2	4.4539	-0.636	-0.7582	5.0502	-1.2469	3.2337	-0.0337	0.1377	0.2254	-0.1335	0.0745	-0.0284	-0.107	0.1206	-0.0541	0.172	0.0011	-0.0398	0.2016	-0.0195	0.2421	60.1608	19.2712	36.846
3	1.4353	1.5377	-2.0506	3.3352	-1.4313	3.4088	0.0302	0.2508	-0.3099	-0.263	-0.1674	-0.0985	0.4494	0.2573	0.168	0.2658	0.049	-0.062	0.3166	-0.0879	0.277	28.2426	6.3087	42.4134
4	3.0327	-0.1105	-0.5735	3.0205	-1.6065	3.9138	-0.082	0.0847	-0.0351	-0.0273	0.0662	0.0547	0.0015	-0.1279	-0.0677	0.1875	0.046	-0.0189	0.1957	-0.0323	0.2285	25.0289	8.6558	51.8277
5	2.6101	0.2035	-0.8097	2.7867	-1.4641	4.1302	0.0292	0.0808	0.0366	0.1138	-0.0048	-0.1045	-0.0768	0.0633	0.0615	0.1687	0.0355	-0.0348	0.1706	-0.0477	0.2606	29.7977	8.5094	50.1158
6	1.4641	1.2517	-1.5193	1.9019	-2.9856	6.6918	-0.1306	0.1205	-0.115	0.5008	0.1799	0.167	0.1064	0	-0.0676	0.3012	0.099	0.0077	0.2552	-0.0208	0.2923	34.421	16.019	31.413
7	8.519	-2.7817	0.7994	4.6084	0.7094	5.2112	-0.4757	0.6968	0.4907	0.3489	0.3292	-0.5322	-0.2325	0.9988	0.1321	0.3272	0.0147	0.0122	0.4787	0.0566	0.3379	64.5253	12.2324	27.5091
8	6.6895	-1.7553	-0.376	2.0984	0.4167	3.1498	0.1718	0.6134	-0.2021	-0.1787	-0.4025	0.1646	0.0229	0.0281	0.1773	0.2077	-0.0035	-0.0646	0.2449	-0.0054	0.2033	48.8765	9.4836	28.9515
9	5.4587	-1.3782	0.0775	2.2731	0.4026	3.3653	0.2011	1.0668	-0.2889	-0.1638	-0.2834	-0.1231	0.2371	0.3326	0.0899	0.2858	0.0627	-0.0109	0.4438	-0.0376	0.2869	56.9917	5.9753	21.7288
10	5.7584	0.5074	-0.664	1.1885	0.4092	5.8669	-0.3092	-0.0458	-0.4715	-0.0682	0.0618	-0.3324	0.3601	-0.0301	0.3068	0.2788	0.0045	0.0048	0.2748	0.0395	0.233	10.6022	7.4661	82.4874
11	5.5558	-1.2125	-1.0498	0.29	-0.0283	2.676	-0.3658	-0.2341	-1.8257	0.0091	-0.0761	-0.2317	1.3347	1.0999	0.4809	0.7907	0.2419	0.1094	0.7542	0.1252	0.5891	26.0129	-2.0711	77.3843
12	9.1999	-0.9422	-1.1847	2.5139	0.353	6.5713	-0.1084	0.6956	-0.3416	-0.3272	-0.0335	0.304	0.0764	0.0826	0.2837	0.4332	-0.0204	-0.0113	0.3659	-0.0204	0.2656	15.7166	8.8296	73.1509
13	5.3212	-0.7597	5.1137	2.2419	-0.0286	5.6733	-0.3561	1.6618	0.0906	-0.3121	-0.0472	0.1765	-0.3772	0.5202	0.4098	0.3451	-0.0987	0.0354	0.5124	0.0327	0.3115	11.2757	12.3067	69.449
14	8.0234	-3.608	-3.211	5.4302	0.4285	5.6515	-0.1013	-0.4226	0.1016	-0.1135	0.2465	-0.6899	-0.6735	0.751	-0.2316	0.3584	0.05	-0.0495	0.4708	-0.0105	0.3477	20.536	15.0939	79.7909
15	2.7313	-4.0368	-1.5563	6.425	1.8662	5.9397	0.0033	-0.1066	0.4372	-0.3713	0.2283	-0.2693	-0.2474	-0.1583	-0.1794	0.2472	0.0049	0.0036	0.3092	0.0566	0.3839	14.1605	13.0709	83.024
16	9.8994	-5.9143	-6.2894	3.7881	4.4513	5.7602	-0.2805	-0.1876	-0.5273	0.1423	-0.0174	0.3902	0.4037	-0.0709	0.2584	0.3278	-0.0194	0.037	0.3016	0.0184	0.2485	17.9814	2.9563	71.154
17	4.4825	-3.2584	-6.2041	5.6695	3.6226	9.3794	-0.2516	1.1957	-1.2695	-0.6494	-0.3915	0.4441	0.3098	-0.4799	0.5755	0.3812	-0.0831	0.0307	0.364	-0.0938	0.4432	12.673	0.3184	71.313
18	8.8685	-2.8985	-3.3919	9.3121	3.7272	5.6667	-0.0542	-0.1536	0.7389	0.0992	-0.1169	0.7351	-0.4752	-0.7406	0.0996	0.3692	0.133	-0.0334	0.5508	0.0117	0.3778	1.0341	17.2867	83.9491
19	4.1029	0.2067	-0.6769	0.5257	-0.0484	2.0258	0.06	-0.4751	0.3566	0.1831	0.0256	-0.052	-0.1255	0.1481	-0.0805	0.2534	0.0316	-0.0517	0.2225	-0.0834	0.289	19.3264	-26.1878	63.6009
20	2.1348	-0.31	0.4041	3.5668	-1.3195	4.369	0.0069	-0.3336	0.5716	0.0383	0.076	0.0044	-0.2871	0.1343	-0.0712	0.2189	-0.0213	-0.0227	0.3263	-0.0877	0.4236	35.5783	-13.3707	35.0317
21	2.7318	-0.1555	-0.7397	2.073	-0.8571	3.8697	-0.0783	0.2329	0.0335	-0.2384	0.0442	-0.0069	0.1568	-0.3078	0.0312	0.1893	0.036	-0.0406	0.2257	-0.0547	0.2859	1.413	-25.6823	47.5168
22	2.5282	-0.7209	-0.3025	2.5617	-0.8825	3.5766	-0.0766	0.1488	0.377	0.0492	0.0354	0.0691	-0.2876	-0.1206	-0.0286	0.2111	0.0552	-0.0276	0.2399	-0.0456	0.3597	0.0136	-18.4577	52.5901
23	2.6073	-0.067	-0.6713	1.8509	-0.8812	3.9102	0.0551	0.1001	0.3702	-0.0739	-0.029	-0.0668	-0.1658	0.0336	0.083	0.178	0.0295	-0.027	0.2087	-0.0306	0.3274	4.9181	-22.0864	50.2302
24	3.3505	1.6605	-3.0284	0.9946	-1.6091	2.7627	0.1851	0.3857	0.7199	0.0466	0.328	0.4416	-0.7136	-0.4553	-0.5076	0.3226	0.0511	0.0058	0.3438	0.0716	0.3068	9.7567	-14.2538	30.8037
25	2.6005	-3.4573	2.1962	7.5007	0.5941	7.6726	-0.2282	0.256	0.4463	0.5769	0.4448	-1.1006	-0.1041	1.1305	-0.0891	0.3287	-0.0313	-0.0531	0.3972	0.0268	0.3699	38.9388	-21.5699	25.986
26	7.466	-4.3625	-2.2578	6.1495	2.1233	1.4039	0.0367	0.1785	0.1014	0.0134	-0.1978	0.1821	0.018	-0.077	0.1869	0.2695	-0.0097	-0.0266	0.3219	0.0566	0.2035	23.6509	-23.4671	26.7362
27	1.1637	-0.8509	-1.2989	7.9359	6.4731	5.6839	0.222	0.0226	-0.1951	-0.4203	-0.4458	0.2775	-0.1137	-0.5492	0.2676	0.3686	0.0009	-0.0769	0.3704	0.0108	0.3018	28.1133	-31.8484	26.9093
28	3.6335	-3.5582	-1.2956	3.499	0.9888	6.5727	-0.2534	-0.4959	0.9425	0.5851	0.0978	0.2107	-1.196	0.2073	0.1522	0.3625	0.014	-0.0265	0.2803	-0.0314	0.4099	16.8104	-11.7681	34.1554
29	7.9058	-3.5828	-1.6492	3.9033	1.1014	3.6977	0.2291	0.6603	-0.2685	-0.1568	-0.2245	-0.0089	0.1714	0.0976	-0.0582	0.2499	-0.0479	-0.0329	0.2653	0.0102	0.2554	30.5124	-27.3233	21.1757
30	6.2872	-1.0021	-1.2773	2.9072	1.565	4.4436	-0.2415	0.1699	-0.271	0.0159	0.0461	0.117	0.1285	-0.1027	0.177	0.2438	-0.0007	-0.0054	0.2534	0.0141	0.2183	-10.941	-24.1001	77.3855
31	8.2678	4.0436	-2.633	2.1298	-2.3907	8.922	0.2629	0.1127	0.8106	0.194	-0.354	-0.1319	-1.6073	1.4377	0.1335	0.9353	0.0788	-0.143	0.8426	0.0485	0.8967	-1.8647	-9.9054	75.0237
32	4.2814	-0.0576	-2.2046	2.0735	2.4383	5.7773	-0.2158	-0.3619	0.4433	0.1874	0.112	-0.2715	0.0405	0.0592	0.0864	0.2708	0.0511	-0.039	0.3468	-0.0081	0.2766	-10.3319	-19.1422	80.828
33	5.3848	-3.4339	-5.1525	4.4256	4.2533	6.5712	-0.2417	0.8494	-0.3596	0.2043	-0.4698	0.6358	0.0981	-1.1707	0.6813	0.2909	-0.0076	-0.0488	0.3674	-0.0405	0.2932	-14.6565	-24.786	75.8908

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 123 )	A	1 - 123
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 124 through 218 )	A	124 - 218
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 18 )	B	1 - 18
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 19 through 75 )	B	19 - 75
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 76 through 101 )	B	76 - 101
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 102 through 113 )	B	102 - 113
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 114 through 128 )	B	114 - 128
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 129 through 174 )	B	129 - 174
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 175 through 212 )	B	175 - 212
10	X-RAY DIFFRACTION	10	chain 'Q' and (resid 31 through 55 )	Q	31 - 55
11	X-RAY DIFFRACTION	11	chain 'Q' and (resid 56 through 62 )	Q	56 - 62
12	X-RAY DIFFRACTION	12	chain 'Q' and (resid 63 through 70 )	Q	63 - 70
13	X-RAY DIFFRACTION	13	chain 'Q' and (resid 71 through 82 )	Q	71 - 82
14	X-RAY DIFFRACTION	14	chain 'Q' and (resid 83 through 99 )	Q	83 - 99
15	X-RAY DIFFRACTION	15	chain 'Q' and (resid 100 through 118 )	Q	100 - 118
16	X-RAY DIFFRACTION	16	chain 'Q' and (resid 119 through 132 )	Q	119 - 132
17	X-RAY DIFFRACTION	17	chain 'Q' and (resid 133 through 139 )	Q	133 - 139
18	X-RAY DIFFRACTION	18	chain 'Q' and (resid 140 through 147 )	Q	140 - 147
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 1 through 123 )	H	1 - 123
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 124 through 217 )	H	124 - 217
21	X-RAY DIFFRACTION	21	chain 'L' and (resid 1 through 38 )	L	1 - 38
22	X-RAY DIFFRACTION	22	chain 'L' and (resid 39 through 75 )	L	39 - 75
23	X-RAY DIFFRACTION	23	chain 'L' and (resid 76 through 102 )	L	76 - 102
24	X-RAY DIFFRACTION	24	chain 'L' and (resid 103 through 113 )	L	103 - 113
25	X-RAY DIFFRACTION	25	chain 'L' and (resid 114 through 128 )	L	114 - 128
26	X-RAY DIFFRACTION	26	chain 'L' and (resid 129 through 150 )	L	129 - 150
27	X-RAY DIFFRACTION	27	chain 'L' and (resid 151 through 163 )	L	151 - 163
28	X-RAY DIFFRACTION	28	chain 'L' and (resid 164 through 174 )	L	164 - 174
29	X-RAY DIFFRACTION	29	chain 'L' and (resid 175 through 212 )	L	175 - 212
30	X-RAY DIFFRACTION	30	chain 'P' and (resid 30 through 82 )	P	30 - 82
31	X-RAY DIFFRACTION	31	chain 'P' and (resid 83 through 94 )	P	83 - 94
32	X-RAY DIFFRACTION	32	chain 'P' and (resid 95 through 127 )	P	95 - 127
33	X-RAY DIFFRACTION	33	chain 'P' and (resid 128 through 147 )	P	128 - 147

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