PDB-12qd: Crystal structure of CM12.1 Fab in complex with an orthomarburgvi...

ID or keywords:

Entry

Database: PDB / ID: 12qd

Title

Crystal structure of CM12.1 Fab in complex with an orthomarburgvirus GP2 peptide

Components

CM12.1 Fab heavy chain
CM12.1 Fab light chain
GP2 peptide

Keywords

IMMUNE SYSTEM / orthomarburgvirus / cross-reactive / antibody / GP2

Function / homology

Function and homology information

fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function

Biological species

Macaca mulatta (Rhesus monkey)

Orthomarburgvirus marburgense

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.47 Å

Authors

Niyongabo, A. / Janus, B.M. / Ofek, G.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of CM12.1 Fab in complex with an orthomarburgvirus GP2 peptide
Authors: Niyongabo, A. / Janus, B.M. / Ofek, G.

History

Deposition	Apr 14, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	12qd.cif.gz	482.7 KB	Display	PDBx/mmCIF format
PDB format	pdb12qd.ent.gz	402.2 KB	Display	PDB format
PDBx/mmJSON format	12qd.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/2q/12qd ftp://data.pdbj.org/pub/pdb/validation_reports/2q/12qd	HTTPS FTP

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Related structure data

Related structure data	12py 12qa 12qb
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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #178 - Oct 2014 Ebola Virus Proteins similarity (3) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

L: CM12.1 Fab light chain

H: CM12.1 Fab heavy chain

B: CM12.1 Fab light chain

A: CM12.1 Fab heavy chain

P: GP2 peptide

C: GP2 peptide

hetero molecules

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

1

L: CM12.1 Fab light chain

H: CM12.1 Fab heavy chain

P: GP2 peptide

hetero molecules

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

2

B: CM12.1 Fab light chain

A: CM12.1 Fab heavy chain

C: GP2 peptide

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.262, 95.723, 150.634
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

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Protein/peptide , 1 types, 2 molecules PC

#3: Protein/peptide	GP2 peptide Mass: 2175.523 Da / Num. of mol.: 2 / Fragment: residues 450-464, with Lys-Lys added to both ends / Source method: obtained synthetically / Source: (synth.) Orthomarburgvirus marburgense / References: UniProt: Q1PDC7

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Antibody , 2 types, 4 molecules LBHA

#1: Antibody	CM12.1 Fab light chain Mass: 23944.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Macaca mulatta (Rhesus monkey)
#2: Antibody	CM12.1 Fab heavy chain Mass: 23053.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Macaca mulatta (Rhesus monkey)

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Non-polymers , 3 types, 259 molecules

#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.78 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.5M Sodium chloride, 0.1M Imidazole/Hydrochloric Acid pH 8.0, 0.2M Zinc acetate, 30% MPD additive

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.47→48.9 Å / Num. obs: 32969 / % possible obs: 97.2 % / Redundancy: 7 % / R_merge(I) obs: 0.17 / Net I/σ(I): 11.1
Reflection shell	Resolution: 2.47→2.6 Å / R_merge(I) obs: 0.565 / Num. unique obs: 3066

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.47→48.89 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 25.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2781	1966	5.96 %
R_work	0.2412	-	-
obs	0.21	32969	97.22 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.47→48.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6627	0	11	248	6886

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003
X-RAY DIFFRACTION	f_angle_d	0.541
X-RAY DIFFRACTION	f_dihedral_angle_d	11.744	2402
X-RAY DIFFRACTION	f_chiral_restr	0.044	1053
X-RAY DIFFRACTION	f_plane_restr	0.004	1191

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 (%)
2.47-2.54	0.3639	130	0.2795	2006	X-RAY DIFFRACTION	90
2.54-2.61	0.3212	135	0.2455	2139	X-RAY DIFFRACTION	95
2.61-2.68	0.2941	139	0.247	2169	X-RAY DIFFRACTION	96
2.68-2.77	0.3278	134	0.239	2111	X-RAY DIFFRACTION	96
2.77-2.87	0.3082	138	0.2517	2189	X-RAY DIFFRACTION	97
2.87-2.98	0.2745	140	0.2341	2174	X-RAY DIFFRACTION	97
2.98-3.12	0.2686	140	0.2213	2198	X-RAY DIFFRACTION	97
3.12-3.28	0.2466	142	0.2008	2240	X-RAY DIFFRACTION	99
3.28-3.49	0.2215	138	0.1957	2237	X-RAY DIFFRACTION	99
3.49-3.76	0.2765	143	0.1742	2251	X-RAY DIFFRACTION	99
3.76-4.13	0.2177	143	0.1714	2268	X-RAY DIFFRACTION	99
4.14-4.73	0.2035	143	0.1481	2262	X-RAY DIFFRACTION	99
4.73-5.96	0.2094	147	0.1892	2332	X-RAY DIFFRACTION	99
5.96-48.89	0.3107	154	0.2658	2427	X-RAY DIFFRACTION	99

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	0.3948	0.3352	0.2848	0.6404	0.2791	0.2053	0.0856	-0.1169	0.142	0.3651	-0.2582	-0.0164	-0.0003	0.1312	-0.2164	0.3074	-0.0288	-0.0106	0.2846	0.0267	0.2228	34.507	34.521	29.305
2	2.0673	0.1148	-0.8576	0.2213	-0.1364	0.4105	0.0945	0.6283	0.5156	-0.0739	-0.1058	-0.368	0.2173	0.0112	0.0566	0.2622	-0.0099	0.0126	0.2098	-0.0493	0.2896	37.991	49.67	15.774
3	0.8983	0.2047	0.7219	0.7149	0.7359	2.0489	0.0927	-0.2109	-0.1795	-0.2416	-0.4276	-0.1906	0.2191	-0.4665	-0.5529	0.2306	-0.0021	0.0401	0.2239	0.0464	0.2718	27.12	32.41	18.491
4	0.8095	0.2454	0.0194	1.3561	0.6774	0.9593	0.0508	-0.043	0.0758	0.1572	-0.0373	0.298	-0.1175	-0.1669	-0.0002	0.1974	0.0203	0.0084	0.1945	0.0189	0.2343	26.347	38.293	24.372
5	-0.0181	0.1917	-0.0559	0.6432	-0.2301	0.06	0.1303	0.2536	0.0624	0.467	0.1374	0.1971	-0.2492	-0.2346	-0.0649	0.2618	0.0005	0.0427	0.2772	-0.0073	0.2115	32.498	29.491	24.939
6	0.7751	0.1688	0.0058	0.8392	-0.5284	0.3494	-0.0642	0.1145	0.0453	-0.1263	-0.0506	0.0642	-0.0046	-0.0661	-0.0374	0.2774	-0.0371	0.0743	0.2277	-0.023	0.2819	26.34	-0.428	28.515
7	0.5031	0.4656	-0.1119	0.4506	-0.0011	0.2664	0.0955	-0.3258	-0.2539	-0.2367	0.0209	0.2121	-0.0716	0.3134	0.0473	0.2702	-0.0149	0.0264	0.2901	0.0263	0.2781	28.76	7.023	30.416
8	0.5028	-0.2574	-0.0132	0.3814	-0.2239	0.2012	-0.1501	0.0281	-0.0712	-0.044	0.2844	-0.6375	0.2275	0.2082	-0.0339	0.3086	0.0262	0.0748	0.1634	-0.0499	0.3419	30.409	-8.522	28.896
9	0.9038	-0.5342	-0.0484	0.3128	0.0005	0.0488	-0.0083	-0.0829	-0.0633	0.1428	0.0507	0.1991	-0.1883	0.0076	0	0.3211	-0.0253	-0.0102	0.2468	-0.0284	0.2603	23.686	-3.044	37.663
10	0.7494	0.1641	0.1683	0.0928	-0.1748	0.7095	0.2094	0.4275	-0.1194	-0.0872	-0.2697	0.0811	-0.0967	-0.0265	-0.0056	0.2794	-0.0445	-0.0048	0.2132	0.0155	0.2839	30.084	26.542	-0.054
11	0.6473	0.5627	-0.2101	1.557	0.0381	0.7483	-0.1158	0.1545	-0.1625	-0.0391	0.1582	-0.0377	-0.2465	0.1666	0.0784	0.1963	-0.0351	0.0446	0.1688	0.0287	0.1952	38.211	30.437	1.894
12	0.2213	-0.2013	-0.3083	0.1985	0.2793	0.3881	-0.2038	0.1253	0.2127	-0.0784	0.1329	-0.2299	0.0949	-0.0718	-0.0101	0.2934	-0.0541	0.003	0.1693	0.0112	0.2881	33.194	29.501	7.81
13	0.4038	0.6924	-0.4189	1.4547	-0.2179	0.8753	-0.0076	0.2036	-0.139	-0.0123	0.0724	-0.0232	0.017	-0.1308	0.1632	0.1645	0.0015	0.017	0.1866	0.0129	0.2101	25.42	5.001	16.627
14	0.4299	-0.0577	-0.3019	0.8226	0.4749	0.3809	-0.3388	0.2654	-0.3044	-0.1294	0.1751	0.0867	0.1648	0.0994	-0.0052	0.1912	-0.0059	0.038	0.2497	0.0247	0.1782	17.108	4.12	16.68
15	1.448	-0.8851	-0.7075	0.6173	0.114	1.7764	-0.3077	0.3707	-0.66	-0.3896	-0.0743	-0.044	0.1584	-0.1347	0.0989	0.3567	-0.1185	0.0075	0.5303	-0.0827	0.303	17.206	-1.919	13.225
16	0.6195	-0.6159	-0.1627	0.6713	0.3804	0.5464	0.0602	-0.0298	0.1249	0.0244	0.0467	0.1382	-0.1447	-0.1181	-0	0.2596	0.0133	-0.0031	0.2518	-0.0112	0.2628	-8.732	36.729	29.558
17	0.6717	0.1335	0.1051	0.563	-0.525	0.5297	0.1591	-0.3428	-0.095	-0.1086	0.0726	-0.4624	-0.125	0.364	0.0612	0.1466	0.0003	0.0435	0.3613	-0.0053	0.2921	2.118	31.68	28.458
18	0.3234	-0.0358	0.3128	0.3203	0.1861	0.5289	-0.019	-0.1826	0.1098	-0.1287	0.0193	0.0123	-0.0927	0.1703	-0	0.2383	0.0054	0.0461	0.2797	-0.0384	0.2787	-2.239	37.168	26.113
19	0.6223	-0.4885	-0.3288	0.3366	0.1379	0.2559	-0.1771	-0.0338	-0.1236	-0.0844	0.0555	-0.0867	0.0492	-0.0032	-0.0004	0.265	-0.0279	0.0654	0.1881	-0.0108	0.2114	-5.386	32.942	20.311
20	0.3801	0.1971	0.0898	2.4525	-0.2562	0.082	0.0315	0.3347	-0.1576	0.1289	-0.2146	-0.4984	0.1346	0.0523	-0.0803	0.3084	-0.035	0.0837	0.4009	-0.0227	0.1993	3.875	15.977	-11.911
21	0.508	-0.0853	0.1835	0.2237	0.4037	0.903	-0.0227	0.4465	0.2972	0.1166	0.0107	0.0135	-0.4036	-0.2617	-0.0328	0.3534	0.0113	0.0504	0.4072	0.0263	0.2974	-1.234	29.244	-6.696
22	1.0417	1.4897	0.3203	2.3697	0.4929	0.2287	0.6376	0.3978	0.3155	0.2536	-0.3838	0.4859	0.2809	-0.1307	-0.0414	0.3074	0.1265	-0.0227	0.438	-0.0055	0.3091	-1.531	29.051	-1.25
23	0.6503	-0.4976	-0.0407	0.4129	-0.0963	0.5028	0.0899	0.3632	0.03	-0.4045	-0.4225	0.3307	-0.3613	-0.5781	-0.1221	0.4748	0.1082	-0.0127	0.51	-0.0174	0.2855	-0.945	25.235	-15.444
24	0.3147	0.212	-0.3033	0.7671	-0.3661	0.8476	-0.276	0.0169	-0.5708	-0.1044	0.0439	-0.2261	-0.0403	0.3357	-0.0393	0.3116	0.0459	0.051	0.272	0.0274	0.342	-1.53	9.346	27.662
25	0.5379	0.075	-0.2684	1.0207	0.5219	0.4044	-0.3178	-0.1731	-0.0393	0.1015	0.2007	-0.0837	-0.2356	-0.5287	-0.0215	0.2722	0.0444	0.0806	0.2894	0.0332	0.2974	-9.895	16.037	30.441
26	0.4252	0.0474	0.3357	0.7199	-0.155	0.3915	-0.0983	-0.5823	-0.6411	0.1379	0.0016	0.2939	0.3184	-0.2454	0.1668	0.1994	-0.0006	0.1335	0.3416	0.0192	0.372	-9.253	7.889	32.09
27	0.5903	-0.6281	0.2395	1.048	0.0597	0.6085	-0.22	-0.2329	0.2658	0.0281	-0.0851	0.1087	0.0132	-0.08	-0.1132	0.2448	0.0754	0.0761	0.2833	-0.0051	0.2472	-5.327	17.548	27.295
28	0.8314	-0.0267	-0.52	0.6808	0.5761	1.3751	-0.0335	0.1066	-0.1095	0.1864	-0.0657	0.0819	-0.0719	0.0589	-0.0082	0.2142	0.0175	-0.0009	0.2707	0.0215	0.2571	2.543	15.499	1.745
29	0.4985	0.2449	0.1307	0.0998	0.092	0.5548	-0.3319	-0.0764	-0.3101	-0.3388	-0.2333	-0.1608	0.4146	0.5377	-0.0147	0.325	0.0814	-0.0007	0.3511	0.0447	0.3406	10.871	10.399	0.458
30	0.1152	0.2993	0.4285	4.5534	2.0755	1.8472	0.3767	0.3574	0.2403	-0.3317	0.2896	-0.286	-0.6335	-0.3906	1.401	0.2567	-0.044	0.0322	0.3389	0.1455	0.2049	33.267	45.367	3.702
31	0.0229	0.0143	0.0233	0.1011	0.1227	0.1415	-0.594	-0.5133	0.8438	0.2181	0.1093	0.3523	0.3042	0.0344	-0.0004	0.5837	0.1454	-0.0052	0.6748	0.0388	0.4315	-5.991	20.024	43.154

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN L AND RESID 1:25 )	L	1 - 25
2	X-RAY DIFFRACTION	2	( CHAIN L AND RESID 26:37 )	L	26 - 37
3	X-RAY DIFFRACTION	3	( CHAIN L AND RESID 38:53 )	L	38 - 53
4	X-RAY DIFFRACTION	4	( CHAIN L AND RESID 54:95 )	L	54 - 95
5	X-RAY DIFFRACTION	5	( CHAIN L AND RESID 96:118 )	L	96 - 118
6	X-RAY DIFFRACTION	6	( CHAIN L AND RESID 119:155 )	L	119 - 155
7	X-RAY DIFFRACTION	7	( CHAIN L AND RESID 156:179 )	L	156 - 179
8	X-RAY DIFFRACTION	8	( CHAIN L AND RESID 180:202 )	L	180 - 202
9	X-RAY DIFFRACTION	9	( CHAIN L AND RESID 203:213 )	L	203 - 213
10	X-RAY DIFFRACTION	10	( CHAIN H AND RESID 1:33 )	H	1 - 33
11	X-RAY DIFFRACTION	11	( CHAIN H AND RESID 34:83 )	H	34 - 83
12	X-RAY DIFFRACTION	12	( CHAIN H AND RESID 84:112 )	H	84 - 112
13	X-RAY DIFFRACTION	13	( CHAIN H AND RESID 113:181 )	H	113 - 181
14	X-RAY DIFFRACTION	14	( CHAIN H AND RESID 182:209 )	H	182 - 209
15	X-RAY DIFFRACTION	15	( CHAIN H AND RESID 210:214 )	H	210 - 214
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 1:37 )	B	1 - 37
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 38:66 )	B	38 - 66
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 67:95 )	B	67 - 95
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 96:118 )	B	96 - 118
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 119:133 )	B	119 - 133
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 134:155 )	B	134 - 155
22	X-RAY DIFFRACTION	22	( CHAIN B AND RESID 156:179 )	B	156 - 179
23	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 180:213 )	B	180 - 213
24	X-RAY DIFFRACTION	24	( CHAIN A AND RESID 1:33 )	A	1 - 33
25	X-RAY DIFFRACTION	25	( CHAIN A AND RESID 34:60 )	A	34 - 60
26	X-RAY DIFFRACTION	26	( CHAIN A AND RESID 61:83 )	A	61 - 83
27	X-RAY DIFFRACTION	27	( CHAIN A AND RESID 84:112 )	A	84 - 112
28	X-RAY DIFFRACTION	28	( CHAIN A AND RESID 113:194 )	A	113 - 194
29	X-RAY DIFFRACTION	29	( CHAIN A AND RESID 195:213 )	A	195 - 213
30	X-RAY DIFFRACTION	30	( CHAIN P AND RESID 455:464 )	P	455 - 464
31	X-RAY DIFFRACTION	31	( CHAIN C AND RESID 456:464 )	C	456 - 464

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Protein/peptide , 1 types, 2 molecules PC

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Antibody , 2 types, 4 molecules LBHA

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Protein/peptide , 1 types, 2 molecules PC

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Antibody , 2 types, 4 molecules LBHA

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Non-polymers , 3 types, 259 molecules

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