PDB-7mf9: Crystal structure of antibody 10E8v4-P100fA Fab in space group C2

ID or keywords:

Entry

Database: PDB / ID: 7mf9

Title

Crystal structure of antibody 10E8v4-P100fA Fab in space group C2

Components

Antibody 10E8v4 Fab heavy chain
Antibody 10E8v4 Fab light chain

Keywords

IMMUNE SYSTEM / Monoclonal antibody 10E8 / MPER / cis-trans isomerization / size-exclusion chromatography

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.7 Å

Authors

Kwon, Y.D. / Kwong, P.D.

Citation

Journal: Antibodies / Year: 2021
Title: Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography.
Authors: Do Kwon, Y. / Wang, X.E. / Bender, M.F. / Yang, R. / Li, Y. / McKee, K. / Rawi, R. / O'Dell, S. / Schneck, N.A. / Shaddeau, A. / Zhang, B. / Arnold, F.J. / Connors, M. / Doria-Rose, N.A. / ...

History

Deposition	Apr 8, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 14, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mf9.cif.gz	822.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7mf9.ent.gz	692.7 KB	Display	PDB format
PDBx/mmJSON format	7mf9.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/mf/7mf9 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/7mf9	HTTPS FTP

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Related structure data

Related structure data	7mf7C 7mf8C 7mfaC 7mfbC 5iq9S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7mf9-5 5awn-d 4qf1-2 5i1d-2 4odu-2 3sgd-2 4ktd-d 7mf9-3 6nb5-2 4rir-2 7mf9-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

S: Starting model for refinement

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: Antibody 10E8v4 Fab heavy chain

L: Antibody 10E8v4 Fab light chain

C: Antibody 10E8v4 Fab heavy chain

D: Antibody 10E8v4 Fab light chain

G: Antibody 10E8v4 Fab heavy chain

I: Antibody 10E8v4 Fab light chain

M: Antibody 10E8v4 Fab heavy chain

N: Antibody 10E8v4 Fab light chain

Q: Antibody 10E8v4 Fab heavy chain

R: Antibody 10E8v4 Fab light chain

240 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: Antibody 10E8v4 Fab heavy chain

L: Antibody 10E8v4 Fab light chain

defined by author&software
Evidence: gel filtration
48.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Antibody 10E8v4 Fab heavy chain

D: Antibody 10E8v4 Fab light chain

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

3

G: Antibody 10E8v4 Fab heavy chain

I: Antibody 10E8v4 Fab light chain

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

4

M: Antibody 10E8v4 Fab heavy chain

N: Antibody 10E8v4 Fab light chain

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

5

Q: Antibody 10E8v4 Fab heavy chain

R: Antibody 10E8v4 Fab light chain

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

Unit cell

Length a, b, c (Å)	160.967, 141.300, 137.413
Angle α, β, γ (deg.)	90.000, 109.170, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Antibody	Antibody 10E8v4 Fab heavy chain Mass: 25111.965 Da / Num. of mol.: 5 / Mutation: Pro100f(kabat numbering)Ala Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-1505 / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens* (human)
#2: Antibody	Antibody 10E8v4 Fab light chain Mass: 22950.463 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
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: 3.07 Å³/Da / Density % sol: 59.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 12% PEG 8000, 0.1M Tris-HCl, 8.5

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Data collection

Diffraction

Mean temperature: 93 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 9, 2019

Radiation

Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.69→50 Å / Num. obs: 24124 / % possible obs: 77.2 % / Redundancy: 2.3 % / B_iso Wilson estimate: 87.54 Å² / R_merge(I) obs: 0.181 / R_pim(I) all: 0.136 / R_rim(I) all: 0.228 / Χ²: 1.034 / Net I/σ(I): 3.9

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
3.7-3.76	1.7	0.541	958	0.649	0.446	0.704	0.663	63.2
3.76-3.83	2	0.482	1063	0.608	0.384	0.62	0.614	67
3.83-3.91	2.1	0.547	1063	0.63	0.415	0.69	0.71	69.6
3.91-3.99	2.2	0.459	1126	0.725	0.345	0.576	0.735	71.7
3.99-4.07	2.2	0.443	1123	0.72	0.33	0.555	0.79	72.5
4.07-4.17	2.3	0.386	1134	0.77	0.285	0.482	0.951	73
4.17-4.27	2.2	0.343	1182	0.821	0.255	0.429	0.995	75.3
4.27-4.39	2.3	0.302	1152	0.859	0.226	0.379	1.229	75
4.39-4.52	2.3	0.275	1185	0.863	0.206	0.346	1.216	76.4
4.52-4.66	2.3	0.273	1226	0.867	0.205	0.343	1.17	77.7
4.66-4.83	2.3	0.238	1204	0.916	0.178	0.299	1.091	77.2
4.83-5.02	2.3	0.233	1215	0.915	0.172	0.291	1.221	78.1
5.02-5.25	2.3	0.224	1260	0.884	0.174	0.285	0.999	80
5.25-5.53	2.2	0.192	1168	0.932	0.15	0.245	0.981	75.5
5.53-5.87	2.4	0.202	1365	0.928	0.152	0.254	0.858	86.7
5.87-6.32	2.6	0.17	1397	0.957	0.124	0.212	0.784	88.5
6.32-6.96	2.6	0.146	1351	0.957	0.107	0.183	0.749	87
6.96-7.96	2.6	0.098	1354	0.979	0.071	0.122	0.883	86.1
7.96-10.02	2.4	0.062	1314	0.991	0.046	0.078	1.341	82.8
10.02-50	2.4	0.057	1284	0.993	0.042	0.071	2.229	79.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.19.1_4122	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IQ9

5iq9

Resolution: 3.7→40.21 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.269	1205	5 %
R_work	0.2401	22902	-
obs	0.2415	24107	76.66 %

Solvent computation

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

Displacement parameters

B_iso max: 191.93 Å² / B_iso mean: 95.6319 Å² / B_iso min: 62.45 Å²

Refinement step

Cycle: final / Resolution: 3.7→40.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16398	0	0	0	16398
Num. residues	-	-	-	-	2157

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.69-3.83	0.3578	107	0.3231	2036	2143	62
3.83-4.01	0.3631	123	0.3202	2332	2455	71
4.01-4.22	0.3537	127	0.2904	2426	2553	73
4.22-4.48	0.2692	133	0.2628	2521	2654	75
4.48-4.83	0.2856	135	0.2447	2557	2692	78
4.83-5.31	0.2915	137	0.227	2600	2737	79
5.31-6.08	0.2728	145	0.233	2751	2896	83
6.08-7.65	0.2446	154	0.2321	2927	3081	87
7.65-40.21	0.1811	144	0.1767	2752	2896	81

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	3.0133	0.1025	-0.8653	2.7335	-0.0216	2.0919	0.156	-0.0519	0.5563	-0.4444	0.0681	-0.402	-0.1172	0.2196	-0.1956	0.72	-0.0669	0.0916	0.6077	-0.1309	0.5666	27.12	6.567	38.734
2	4.0591	3.0974	-2.1956	2.555	-1.147	2.89	1.0546	-0.4377	0.9038	0.5617	-0.3544	0.2997	-1.0909	-0.2304	-1.0959	0.8312	0.0391	-0.132	0.7925	-0.0885	0.9635	-3.389	12.434	58.051
3	0.64	-0.3801	-1.0379	1.6968	-0.1272	1.9576	-0.2741	-0.3487	-0.3663	0.2279	0.1453	0.0463	0.1868	0.2705	0.0486	0.6342	-0.0583	-0.0835	0.9751	0.0119	0.5898	-5.651	23.905	22.742
4	5.6193	-1.5595	-4.8994	8.4659	5.6601	6.6296	0.1927	0.1799	-0.9427	0.5905	-0.1773	1.6543	0.2471	-0.2798	0.0477	0.8721	0.091	-0.0379	0.954	0.3167	1.1127	-35.292	19.258	44.059
5	2.4713	1.7903	-2.4353	1.3619	-0.9605	4.9022	-0.1945	-0.0402	-0.5999	-0.6158	-0.2742	-0.0582	0.2853	-0.1573	0.269	0.649	0.0734	-0.0757	0.6311	-0.007	0.6981	-1.279	-8.14	21.944
6	5.9246	-1.0889	2.522	7.6081	0.8402	1.4379	0.4751	0.6533	-0.8478	-1.1167	-0.4193	-0.4602	0.3783	0.3619	0.0615	0.9301	0.2279	0.0507	0.9724	0.124	0.5822	26.871	-5.645	-0.951
7	3.3276	0.4079	-0.6744	1.2242	-0.3304	1.4691	0.1499	-0.3858	0.3025	-0.0376	-0.2531	-0.2418	0.1969	0.2686	0.0848	0.6595	-0.1023	-0.1211	0.7241	-0.1441	0.7269	52.862	29.733	45.272
8	0.3807	-0.6698	-0.9814	1.0644	1.8022	5.3341	-0.0257	0.0775	-0.2585	0.101	-0.4327	0.5788	0.1752	-1.2273	0.4684	0.8645	-0.2308	-0.1422	1.1762	-0.2672	1.2957	20.968	27.934	64.065
9	1.6876	0.2982	-0.2796	1.4056	-0.3232	1.7964	-0.1993	-0.9863	0.1136	0.622	0.0663	0.1458	-0.1944	0.2233	0.0073	0.8258	0.0124	0.0548	1.0669	-0.1681	0.6198	68.305	-16.914	42.253
10	1.1894	-1.1404	0.1505	3.0365	1.9144	2.2191	0.2897	-1.0561	0.2898	-0.3115	-0.0418	0.4139	-0.5949	0.9196	-0.0032	0.7158	-0.1412	-0.223	1.4943	-0.2012	0.9408	101.701	-15.876	27.856
11	3.4369	0.5233	-0.5491	3.0874	-1.2618	6.2856	0.0838	-0.4637	0.1531	0.3937	-0.0242	0.1775	0.23	0.0792	-0.0559	0.3577	-0.0327	0.0164	0.7315	-0.0768	0.628	28.797	-8.395	53.004
12	7.7575	-0.1601	1.7319	3.6741	-0.0707	3.1464	0.0992	-0.7299	-0.1655	0.2159	-0.1238	0.8617	0.129	-0.0721	0.0717	0.6252	-0.0339	0.2716	0.7594	-0.1195	0.8299	-1.981	-3.62	52.67
13	6.1502	1.7875	-2.6284	3.7845	-1.0944	2.1955	-0.3547	0.4812	0.1762	-0.1346	0.0671	0.466	0.14	-0.3304	0.271	0.5774	-0.0468	-0.2155	0.6861	0.0169	0.491	-21.116	26.82	9.086
14	3.5001	1.2342	-0.6457	5.5572	0.8915	5.4473	-0.0089	0.0111	-0.259	0.2871	0.0981	0.0474	-0.463	-0.1785	-0.067	0.6707	0.1879	0.1037	0.7882	0.1389	0.6928	-35.5	34.024	36.036
15	7.502	-4.3321	-1.8825	5.203	0.4775	5.7922	-0.2664	0.3232	-0.8845	-0.2775	0.1795	-0.116	0.3352	-0.1019	0.1636	0.8082	-0.1215	-0.0132	0.5885	-0.1481	0.5257	5.8	-27.729	22.418
16	8.7495	5.8684	1.0447	7.7072	-0.6713	2.1938	-0.1628	0.344	-0.6346	0.1825	0.0711	-0.5133	0.3092	0.2263	0.0806	0.7456	0.1042	0.1641	0.8147	0.0012	0.6042	31.487	-12.231	14.093
17	6.4982	-3.2315	-2.0138	5.2425	2.0349	4.3149	-0.0827	0.6609	0.2767	0.3758	-0.2684	0.4245	0.0347	-0.0465	0.5781	0.5307	-0.1196	0.0391	0.672	-0.0716	0.6084	47.817	49.856	46.793
18	1.5871	1.5967	1.1438	6.1896	-1.2913	4.2244	0.1035	-0.1095	-0.1254	0.458	-0.3182	0.5616	0.5149	-0.5963	0.2458	0.6947	-0.171	0.2935	1.0587	-0.2168	0.9457	32.108	38.339	71.052
19	7.9634	4.6603	-1.1448	7.5793	-2.9981	2.9065	0.4434	-0.2937	0.9346	-0.1475	-0.1325	0.1772	-0.2963	0.1132	-0.2449	0.6583	0.0491	0.0754	0.8373	-0.1374	0.586	65.255	-4.291	25.99
20	3.4867	-3.6674	-1.8644	6.6676	0.8545	4.9481	-0.1513	-0.3889	0.5096	0.2038	0.4082	-0.6638	-0.3106	0.3143	-0.1109	0.5512	-0.1811	0.0559	1.0122	-0.1236	0.7009	90.21	-20.247	16.245

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN H AND RESID 1:126 )	H	1 - 126
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 136:214 )	H	136 - 214
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 1:126 )	C	1 - 126
4	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 138:214 )	C	138 - 214
5	X-RAY DIFFRACTION	5	( CHAIN G AND RESID 1:126 )	G	1 - 126
6	X-RAY DIFFRACTION	6	( CHAIN G AND RESID 138:214 )	G	138 - 214
7	X-RAY DIFFRACTION	7	( CHAIN M AND RESID 1:126 )	M	1 - 126
8	X-RAY DIFFRACTION	8	( CHAIN M AND RESID 135:214 )	M	135 - 214
9	X-RAY DIFFRACTION	9	( CHAIN Q AND RESID 1:126 )	Q	1 - 126
10	X-RAY DIFFRACTION	10	( CHAIN Q AND RESID 137:214 )	Q	137 - 214
11	X-RAY DIFFRACTION	11	( CHAIN L AND RESID 2:113 )	L	2 - 113
12	X-RAY DIFFRACTION	12	( CHAIN L AND RESID 114:209 )	L	114 - 209
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 3:113 )	D	3 - 113
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 114:209 )	D	114 - 209
15	X-RAY DIFFRACTION	15	( CHAIN I AND RESID 3:113 )	I	3 - 113
16	X-RAY DIFFRACTION	16	( CHAIN I AND RESID 114:209 )	I	114 - 209
17	X-RAY DIFFRACTION	17	( CHAIN N AND RESID 3:113 )	N	3 - 113
18	X-RAY DIFFRACTION	18	( CHAIN N AND RESID 114:209 )	N	114 - 209
19	X-RAY DIFFRACTION	19	( CHAIN R AND RESID 3:113 )	R	3 - 113
20	X-RAY DIFFRACTION	20	( CHAIN R AND RESID 114:209 )	R	114 - 209

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