PDB-6qcu: Crystal structure of a Fab portion of the anti EBOV 3T0331 antibody

ID or keywords:

Entry

Database: PDB / ID: 6qcu

Title

Crystal structure of a Fab portion of the anti EBOV 3T0331 antibody

Components

Heavy chain
Light chain

Keywords

IMMUNE SYSTEM /

Antibody /

immune response /

viral infection /

EBOV

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: 1.56 Å

Authors

Diskin, R. / Cohen-Dvashi, H.

Citation

Journal: Nat.Med. (N.Y.) / Year: 2019
Title: rVSV-ZEBOV induces a polyclonal and convergent B cell response with potent Ebola virus-neutralizing antibodies
Authors: Diskin, R. / Cohen-Dvashi, H. / Ehrhardt, S. / Zehner, M. / Krahling, V. / Kreer, C. / Dahlke, C. / Ercanoglu, M.S. / Gruell, H. / Addo, M.M. / Becker, S. / Klein, F.

History

Deposition	Dec 31, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 2, 2019	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6qcu.cif.gz	254.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6qcu.ent.gz	218.5 KB	Display	PDB format
PDBx/mmJSON format	6qcu.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/qc/6qcu ftp://data.pdbj.org/pub/pdb/validation_reports/qc/6qcu	HTTPS FTP

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Related structure data

Similar structure data	1nak-1 5tdo-2 3i75-d 6u3z-2 3g6j-4 5nbw-1 6dwa-1 4lou-3 6tco-2 2gcy-d 4kk6-3 1uyw-1 4r7n-9 6pxg-3 6tco-1 6ug9-2 5vzr-1 6z3k-3 6z7x-d 1y0l-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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)

Deposited unit

L: Light chain

H: Heavy chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	91.095, 91.095, 215.434
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	H-607- HOH
2	1	H-625- HOH

#1: Antibody	Light chain / Mass: 23310.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody	Heavy chain Mass: 23673.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.75 Å³/Da / Density % sol: 55.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.15M LiSo4 monohydrate, 0.1M Citric Acid pH3.5, 18% PEG 6000, 5% Ethylen Glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 5, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.56→78.9 Å / Num. obs: 75996 / % possible obs: 100 % / Redundancy: 13 % / B_iso Wilson estimate: 18.56 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.1322 / R_pim(I) all: 0.03836 / R_rim(I) all: 0.1378 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.56→1.616 Å / Redundancy: 13.2 % / Num. unique obs: 7436 / CC_1/2: 0.863 / R_pim(I) all: 0.2539 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3297: ???)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.56→78.891 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.25

	R_factor	Num. reflection	% reflection
R_free	0.2027	3769	4.97 %
R_work	0.1758	-	-
obs	0.1771	75878	99.97 %

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å

Refinement step

Cycle: LAST / Resolution: 1.56→78.891 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3265	0	20	507	3792

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3375
X-RAY DIFFRACTION	f_angle_d	1.144	4605
X-RAY DIFFRACTION	f_dihedral_angle_d	2.967	2754
X-RAY DIFFRACTION	f_chiral_restr	0.064	520
X-RAY DIFFRACTION	f_plane_restr	0.008	590

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 (%)
1.5597-1.5794	0.3319	131	0.2953	2626	X-RAY DIFFRACTION	99
1.5794-1.6002	0.3364	120	0.2837	2632	X-RAY DIFFRACTION	100
1.6002-1.6221	0.2821	148	0.2782	2595	X-RAY DIFFRACTION	100
1.6221-1.6453	0.283	141	0.2676	2618	X-RAY DIFFRACTION	100
1.6453-1.6698	0.2749	126	0.2422	2627	X-RAY DIFFRACTION	100
1.6698-1.6959	0.2739	146	0.2335	2626	X-RAY DIFFRACTION	100
1.6959-1.7238	0.2393	136	0.2262	2631	X-RAY DIFFRACTION	100
1.7238-1.7535	0.2536	130	0.2183	2659	X-RAY DIFFRACTION	100
1.7535-1.7854	0.2277	139	0.2	2638	X-RAY DIFFRACTION	100
1.7854-1.8197	0.2418	152	0.2118	2598	X-RAY DIFFRACTION	100
1.8197-1.8569	0.2258	155	0.2129	2637	X-RAY DIFFRACTION	100
1.8569-1.8972	0.2432	150	0.208	2621	X-RAY DIFFRACTION	100
1.8972-1.9414	0.2417	135	0.1865	2629	X-RAY DIFFRACTION	100
1.9414-1.9899	0.2363	134	0.1792	2654	X-RAY DIFFRACTION	100
1.9899-2.0437	0.2143	145	0.1752	2625	X-RAY DIFFRACTION	100
2.0437-2.1039	0.2096	149	0.1766	2651	X-RAY DIFFRACTION	100
2.1039-2.1718	0.1809	134	0.1651	2683	X-RAY DIFFRACTION	100
2.1718-2.2494	0.1951	131	0.1589	2647	X-RAY DIFFRACTION	100
2.2494-2.3395	0.1712	136	0.1555	2692	X-RAY DIFFRACTION	100
2.3395-2.446	0.1818	147	0.1519	2647	X-RAY DIFFRACTION	100
2.446-2.5749	0.1666	120	0.1553	2700	X-RAY DIFFRACTION	100
2.5749-2.7363	0.1752	134	0.1632	2709	X-RAY DIFFRACTION	100
2.7363-2.9475	0.1752	124	0.1628	2727	X-RAY DIFFRACTION	100
2.9475-3.2442	0.1985	155	0.1635	2710	X-RAY DIFFRACTION	100
3.2442-3.7136	0.1779	144	0.1617	2756	X-RAY DIFFRACTION	100
3.7136-4.6787	0.1832	140	0.1412	2797	X-RAY DIFFRACTION	100
4.6787-78.992	0.2	167	0.1872	2974	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	2.5052	-0.827	-1.026	0.9826	0.1974	1.1667	0.0109	0.0318	0.0318	0.0313	-0.0251	-0.0018	0.0104	-0.0142	0.014	0.1357	-0.0088	-0	0.1098	-0.0056	0.0958	-28.3226	59.8846	2.0494
2	2.5803	-0.5451	-2.2086	3.0179	2.4816	3.5172	0.3095	0.2028	0.225	-0.273	-0.1482	-0.3066	-0.1971	0.0208	-0.0471	0.1507	-0.0047	0.0095	0.1264	0.0301	0.0801	-17.8492	44.8625	-8.6373
3	1.7954	0.9316	-0.7985	3.3109	-0.4767	1.7744	-0.1534	0.1211	-0.3031	0.0222	-0.0149	0.1556	0.4222	-0.2111	0.0792	0.217	-0.0203	0.0479	0.1448	-0.0369	0.1904	-22.2205	23.2496	-8.382
4	1.3387	1.4166	-0.2477	3.2967	-0.2758	0.7695	0.0359	-0.0717	-0.1284	0.0217	-0.0716	-0.2595	-0.0484	0.0415	0.0193	0.1081	0	0.0101	0.131	-0.0027	0.1195	-39.2586	49.9585	18.2973
5	5.0177	-0.3092	-1.7823	1.0986	0.4996	1.677	-0.1317	-0.3247	-0.3038	0.3362	-0.0164	0.1512	0.3639	0.2023	0.1234	0.3173	0.0032	0.0696	0.1581	0.0292	0.1748	-22.0219	24.465	7.5077

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 101 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 102 through 113 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 114 through 211 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 2 through 116 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 117 through 219 )

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