PDB-5ggu: Crystal structure of tremelimumab Fab

ID or keywords:

Entry

Database: PDB / ID: 5ggu

Title

Crystal structure of tremelimumab Fab

Components

heavy chain
light chain

Keywords

IMMUNE SYSTEM /

antibody

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.292 Å

Authors

Heo, Y.S.

Citation

Journal: Nat Commun / Year: 2016
Title: Structural basis of checkpoint blockade by monoclonal antibodies in cancer immunotherapy
Authors: Lee, J.Y. / Lee, H.T. / Shin, W. / Chae, J. / Choi, J. / Kim, S.H. / Lim, H. / Won Heo, T. / Park, K.Y. / Lee, Y.J. / Ryu, S.E. / Son, J.Y. / Lee, J.U. / Heo, Y.S.

History

Deposition	Jun 16, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ggu.cif.gz	342.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5ggu.ent.gz	293.1 KB	Display	PDB format
PDBx/mmJSON format	5ggu.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/gg/5ggu ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggu	HTTPS FTP

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Related structure data

Related structure data	5ggqC 5ggrC 5ggsC 5ggtC 5ggvC C: citing same article (ref.)
Similar structure data	5d1z-2 6lun-2 4xbp-4 3cfj-2 4kvc-d 1n7m-d 1dqq-1 1vpo-d 2fjf-10 4m6m-d 3j3z-d 5e2w-d 1y18-2 5bk5-4 4xcy-3 2ddq-d 4odu-1 4nzu-d 6phh-1 2f5a-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 - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: heavy chain

L: light chain

A: heavy chain

B: light chain

98.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: heavy chain

L: light chain

defined by author&software
49.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: heavy chain

B: light chain

defined by author&software
49.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.691, 103.211, 184.748
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	H-350- HOH

#1: Antibody	heavy chain Mass: 25951.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody	light chain / Mass: 23406.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.38 Å³/Da / Density % sol: 48.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50 mM Tris, pH 8.5, 30% PEG4,000, 0.2 M ammonium chloride, 10 mM CaCl2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.29→50 Å / Num. obs: 42405 / % possible obs: 99.8 % / Redundancy: 6.1 % / Net I/σ(I): 28.1

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.292→35.665 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26

	R_factor	Num. reflection	% reflection
R_free	0.2431	2140	5.05 %
R_work	0.1845	-	-
obs	0.1876	42405	99.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.292→35.665 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6602	0	0	347	6949

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6772
X-RAY DIFFRACTION	f_angle_d	1.222	9208
X-RAY DIFFRACTION	f_dihedral_angle_d	14.224	2412
X-RAY DIFFRACTION	f_chiral_restr	0.044	1024
X-RAY DIFFRACTION	f_plane_restr	0.006	1178

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2917-2.345	0.3359	117	0.2489	2446	X-RAY DIFFRACTION	92
2.345-2.4037	0.2995	146	0.2386	2656	X-RAY DIFFRACTION	100
2.4037-2.4687	0.3155	139	0.2319	2704	X-RAY DIFFRACTION	100
2.4687-2.5413	0.3466	135	0.2318	2658	X-RAY DIFFRACTION	100
2.5413-2.6233	0.326	153	0.2355	2660	X-RAY DIFFRACTION	100
2.6233-2.717	0.3139	144	0.2255	2690	X-RAY DIFFRACTION	100
2.717-2.8257	0.2976	122	0.2241	2688	X-RAY DIFFRACTION	100
2.8257-2.9543	0.2767	148	0.2088	2688	X-RAY DIFFRACTION	100
2.9543-3.11	0.2726	148	0.2158	2688	X-RAY DIFFRACTION	100
3.11-3.3047	0.2595	133	0.1956	2670	X-RAY DIFFRACTION	100
3.3047-3.5596	0.2381	141	0.1713	2734	X-RAY DIFFRACTION	100
3.5596-3.9174	0.2142	164	0.1634	2677	X-RAY DIFFRACTION	100
3.9174-4.4834	0.1794	155	0.1407	2716	X-RAY DIFFRACTION	100
4.4834-5.645	0.178	140	0.1348	2739	X-RAY DIFFRACTION	100
5.645-35.669	0.2241	155	0.1763	2851	X-RAY DIFFRACTION	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	2.8759	-0.0627	-0.0972	3.241	0.3893	1.1724	0.1458	0.2074	0.3796	0.4573	0.0291	-0.49	-0.1082	-0.0509	-0.0887	0.3093	0.0597	-0.0744	0.286	0.0062	0.3281	22.127	82.2477	41.5008
2	2.9432	0.8002	0.3618	1.8478	-0.2512	1.6641	0.0375	-0.3087	0.2863	-0.1244	-0.071	0.1845	-0.0074	-0.0872	0.0122	0.1904	0.0184	-0.0539	0.2242	-0.019	0.1625	14.2129	91.5658	38.0563
3	1.6113	0.8331	0.1963	3.3352	0.1837	2.2363	-0.8946	-0.2455	0.0864	0.8478	-0.1687	0.0266	1.2995	-0.2099	0.3565	-0.0531	0.1026	-0.2311	0.3129	-0.0366	0.215	10.9372	88.2906	43.8103
4	1.8272	-1.6734	-0.6551	1.9964	0.3744	2.3077	-0.4728	-0.1413	0.0581	-0.0597	0.1464	0.0294	0.1497	-0.006	0.2429	0.3477	-0.0077	-0.0213	0.2606	-0.0023	0.2142	14.1559	81.3832	42.5064
5	0.7999	-0.4255	-0.0803	3.1207	-0.8178	0.6721	0.035	0.0425	0.1286	-0.1367	-0.0995	-0.0419	-0.0869	-0.0058	0.108	0.2431	-0.0249	-0.0498	0.208	-0.0426	0.2454	14.5055	99.1026	31.1984
6	1.2243	-0.2738	-0.5599	1.2659	0.2245	0.9471	-0.1415	0.0633	0.0627	0.1543	0.1054	-0.1114	-0.0413	0.0649	0.0101	0.1913	-0.0331	-0.0581	0.2136	0.0152	0.1887	27.611	68.284	28.8296
7	1.1167	-0.292	-0.185	1.7347	-0.1375	0.9419	-0.0906	0.1719	-0.1214	0.0095	0.0404	-0.1954	-0.0927	0.1181	0.039	0.2678	-0.1131	-0.0266	0.3464	-0.0395	0.214	32.3352	65.6841	22.4883
8	1.797	-1.0695	-1.9369	1.4293	0.8327	4.1438	-0.1578	-0.4433	-0.4548	0.1046	0.1606	-0.459	0.1126	1.0221	-0.048	0.2374	-0.0549	-0.0824	0.4513	-0.0791	0.5303	40.8457	61.2432	25.5247
9	4.0679	-0.1829	-3.4561	1.7666	1.2176	3.0962	0.1224	0.2249	0.0452	-0.5299	-0.0219	0.1483	-0	-0.0908	0.0236	0.4658	0.0383	-0.0268	0.261	0.077	0.2022	11.3173	86.9501	12.7501
10	1.5743	-0.4377	-0.5358	1.7959	0.2143	1.9175	0.0314	0.0619	0.2786	-0.5182	-0.0086	-0.2219	-0.2279	-0.0026	-0.0425	0.374	-0.0043	-0.0178	0.2092	0.0569	0.3249	12.9049	95.4084	19.033
11	1.4062	0.0062	0.1829	1.3173	0.1404	2.0113	-0.1215	0.1033	0.1499	-0.4225	0.0429	-0.1663	-0.2537	-0.1002	0.0272	0.3618	-0.039	-0.0058	0.1962	0.064	0.2698	12.7862	91.555	18.8068
12	0.113	-0.5136	-0.3078	1.049	0.6666	0.3311	0.3673	-0.157	0.2187	-0.4455	-0.0195	-0.1391	0.0532	-0.0532	-0.1906	0.683	-0.0738	0.1117	0.3018	0.0119	0.2744	22.1156	77.5987	5.9123
13	0.72	0.7878	-1.04	3.3105	-1.093	2.2484	0.0246	0.1326	0.016	0.067	0.039	-0.0648	-0.2897	0.2057	-0.0735	0.1958	-0.0652	-0.023	0.279	0.0115	0.2057	24.9386	57.5369	14.9656
14	1.5441	1.4538	0.2707	3.5682	0.8066	0.4335	0.1391	0.1615	-0.0988	-0.871	-0.2026	0.1012	-0.2581	-0.2946	-0.138	0.254	0.012	-0.0517	0.2908	-0.0176	0.2209	15.9298	55.3473	16.7002
15	1.0701	-0.0655	-0.1265	2.1748	-0.7859	2.2637	0.006	0.1805	0.0738	0.1355	-0.0203	-0.0178	-0.3046	0.1945	-0.0117	0.1531	-0.0377	-0.015	0.2504	-0.0233	0.2368	23.3411	58.071	15.0106
16	1.8665	-0.2749	1.2842	4.7362	-1.33	3.8051	0.2111	0.4084	-0.1352	-1.3313	-0.3424	0.0966	0.4441	0.2843	0.2002	0.2452	-0.0509	0.0474	0.4073	-0.0265	0.1902	22.9534	54.1293	5.671
17	2.6656	0.0634	0.3839	3.2818	0.0625	1.3629	0.1607	-0.1803	-0.0398	0.8736	-0.0015	0.4419	0.3036	0.0234	-0.1209	0.2706	0.0634	0.0114	0.3293	-0.0336	0.1271	7.2803	38.6962	42.9222
18	1.9855	1.4526	-0.0743	2.1059	0.3516	1.7126	-0.0441	-0.1879	-0.3075	0.4084	-0.0489	-0.4128	0.081	0.0206	0.0457	0.2168	0.0308	-0.0484	0.2072	0.0127	0.1814	13.7046	29.3613	37.6985
19	1.8751	0.4193	-0.5364	4.9834	-0.1242	2.9585	0.0739	0.0334	-0.0591	0.6131	0.204	-0.3698	0.202	0.418	-0.0419	0.2648	0.011	-0.1774	0.1932	0.1089	0.3222	18.1582	32.5571	42.4187
20	0.7231	-0.5178	0.3516	1.9243	-0.0143	2.2541	-0.1993	-0.3138	-0.0242	-0.0027	0.2578	-0.102	0.2783	0.1338	-0.0591	0.2222	0.0659	-0.0824	0.2712	0.0105	0.2169	15.0553	39.5011	41.998
21	0.185	-0.1572	0.324	2.0917	0.4004	0.7134	0.0174	-0.1133	-0.329	0.263	0.1855	-0.2969	0.1677	0.0543	-0.0543	0.177	-0.0138	-0.0252	0.1679	0.0045	0.3105	11.72	21.8418	31.1032
22	1.5893	1.3748	0.0809	3.6747	1.5653	0.9972	-0.0948	-0.3312	-0.0267	0.0905	0.0025	0.0821	0.1714	0.1273	0.1261	0.1933	0.0183	-0.0779	0.1976	0.0095	0.2317	6.5766	35.1035	35.1358
23	2.7429	-1.4723	1.6758	1.6523	-1.084	1.8028	-0.1535	-0.085	0.426	0.174	-0.1015	0.0465	-0.198	0.0099	0.1088	0.2196	-0.0573	-0.0352	0.2248	-0.0098	0.1813	-4.4887	61.2037	30.5806
24	1.6491	0.1259	0.5156	1.2486	0.3984	0.8319	0.2226	0.2553	0.2268	0.1678	-0.1675	0.0986	0.136	-0.0887	-0.0438	0.3034	-0.0088	0.0127	0.288	-0.0081	0.1322	-6.7938	55.138	27.0806
25	3.292	-0.0139	2.4278	1.6058	-0.1904	3.1423	0.1373	-0.6894	-0.0043	0.3467	0.1065	0.6153	0.0345	-0.7585	-0.2144	0.2287	0.0332	0.0602	0.3193	0.0219	0.308	-14.2855	59.2352	32.1821
26	4.5898	-0.7684	1.7067	1.9344	-0.9607	1.7908	0.033	0.072	0.1297	-0.5372	-0.1055	-0.2088	0.1637	0.2123	0.0433	0.1791	0.0045	-0.028	0.2746	-0.007	0.2492	11.066	34.1019	12.3515
27	1.458	0.357	0.4814	1.5129	-0.2895	1.2769	0.0618	0.0578	-0.3116	-0.1495	-0.0147	-0.0954	0.0562	-0.0184	-0.0513	0.1841	0.0041	-0.0402	0.1923	-0.0509	0.249	10.9183	25.5863	18.8229
28	1.4811	-0.6664	0.3303	1.6792	-0.2772	1.2616	0.19	-0.0716	-0.2783	-0.2003	-0.0148	0.0624	0.1773	-0.0178	-0.1962	0.1589	-0.0309	-0.0318	0.1758	-0.029	0.2592	11.0733	29.4092	18.5997
29	0.9388	-1.873	0.9133	2.8771	-1.4716	0.7108	0.2244	-0.0144	0.0718	0.0853	0.2318	0.1635	0.1213	-0.2551	-0.0813	0.2865	-0.0203	-0.1239	0.2571	-0.0681	0.1611	-0.953	43.5618	8.4917
30	0.5451	0.7135	0.4296	3.2163	0.6511	1.2887	0.0207	0.1443	0.1006	0.1071	0.0135	0.0538	-0.0883	-0.0985	-0.0189	0.211	0.0223	-0.0595	0.2564	0.0239	0.1486	-1.3386	63.3849	18.3078
31	0.9503	1.0698	-0.5182	2.8813	-0.5567	0.4158	-0.2604	0.2206	-0.0062	-0.2693	-0.0608	-0.324	-0.3012	-0.051	0.1539	0.325	-0.0006	0.0155	0.3166	0.1238	0.2351	7.8678	65.6244	17.8083
32	1.0735	0.2361	0.4661	3.2372	0.9322	1.2992	0.0733	0.1803	0.0528	0.0163	-0.1086	0.1345	-0.0049	-0.1684	0.0208	0.2015	0.009	-0.0322	0.2492	-0.0029	0.1854	0.0749	62.8884	17.904
33	1.293	0.2638	0.16	4.328	2.0363	2.7021	-0.1066	0.1899	0.4649	-0.885	-0.0692	0.1366	-0.6959	-0.2892	0.1826	0.3592	0.0346	-0.1529	0.2916	0.0313	0.2913	-1.4287	66.9418	8.9076

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 60 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 61 through 76 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 77 through 91 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 92 through 111 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 112 through 157 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 158 through 200 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 201 through 225 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 1 through 18 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 19 through 69 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 70 through 101 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 102 through 113 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 114 through 150 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 151 through 163 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 164 through 197 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 198 through 213 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 1 through 17 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 18 through 60 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 61 through 76 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 77 through 91 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 92 through 111 )
22	X-RAY DIFFRACTION	22	chain 'A' and (resid 112 through 123 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 124 through 157 )
24	X-RAY DIFFRACTION	24	chain 'A' and (resid 158 through 200 )
25	X-RAY DIFFRACTION	25	chain 'A' and (resid 201 through 225 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 1 through 18 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 19 through 69 )
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 70 through 101 )
29	X-RAY DIFFRACTION	29	chain 'B' and (resid 102 through 113 )
30	X-RAY DIFFRACTION	30	chain 'B' and (resid 114 through 150 )
31	X-RAY DIFFRACTION	31	chain 'B' and (resid 151 through 163 )
32	X-RAY DIFFRACTION	32	chain 'B' and (resid 164 through 197 )
33	X-RAY DIFFRACTION	33	chain 'B' and (resid 198 through 213 )

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-Movie

-Structure viewers

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-This page

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

-
This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi