PDB-5ywf: Crystal structure of 2H4 Fab

ID or keywords:

Entry

Database: PDB / ID: 5ywf

Title

Crystal structure of 2H4 Fab

Components

2H4 heavy chain
2H4 light chain

Keywords

IMMUNE SYSTEM /

Flaviviruses /

Viral encephalitis / neutralizing monoclonal antibodies /

structural analysis /

viral entry

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.206 Å

Authors

Qiu, X. / Lei, Y. / Yang, P. / Gao, Q. / Wang, N. / Cao, L. / Wang, X. / Xu, Z.K. / Rao, Z.

Funding support

China, 1items

Citation

Journal: Nat Microbiol / Year: 2018
Title: Structural basis for neutralization of Japanese encephalitis virus by two potent therapeutic antibodies.
Authors: Xiaodi Qiu / Yingfeng Lei / Pan Yang / Qiang Gao / Nan Wang / Lei Cao / Shuai Yuan / Xiaofang Huang / Yongqiang Deng / Wenyu Ma / Tianbing Ding / Fanglin Zhang / Xingan Wu / Junjie Hu / Shan- ...
Abstract: Japanese encephalitis virus (JEV), closely related to dengue, Zika, yellow fever and West Nile viruses, remains neglected and not well characterized . JEV is the leading causative agent of ...

History

Deposition	Nov 29, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ywf.cif.gz	339 KB	Display	PDBx/mmCIF format
PDB format	pdb5ywf.ent.gz	288.8 KB	Display	PDB format
PDBx/mmJSON format	5ywf.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/yw/5ywf ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywf	HTTPS FTP

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Related structure data

Related structure data	6854C 6855C 5ywoC 5ywpC C: citing same article (ref.)
Similar structure data	6co3-d 5it2-d 4qth-2 6mee-1 6p9i-1 6al4-3 6ws6-3 1kem-d 4h20-d 5vh3-1 1flr-d 6c5i-d 6btj-2 15c8-d 4nm4-1 4m7z-1 6srx-2 3nab-d 6d0x-d 2d03-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

A: 2H4 light chain

B: 2H4 heavy chain

C: 2H4 light chain

D: 2H4 heavy chain

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

1

A: 2H4 light chain

B: 2H4 heavy chain

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

2

C: 2H4 light chain

D: 2H4 heavy chain

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

Unit cell

Length a, b, c (Å)	44.366, 140.980, 78.959
Angle α, β, γ (deg.)	90.00, 91.22, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	2H4 light chain Mass: 23840.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody	2H4 heavy chain Mass: 23337.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.61 Å³/Da / Density % sol: 52.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16% (w/v) PEG3350, 2% Tacsimate, 0.1 M sodium acetate pH 4.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9778 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 48459 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 10.17
Reflection shell	Resolution: 2.2→2.28 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.206→44.356 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 29.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2618	2379	4.91 %
R_work	0.2155	-	-
obs	0.2178	48414	99.36 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.206→44.356 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6565	0	0	207	6772

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6790
X-RAY DIFFRACTION	f_angle_d	1.445	9266
X-RAY DIFFRACTION	f_dihedral_angle_d	17.218	4040
X-RAY DIFFRACTION	f_chiral_restr	0.074	1036
X-RAY DIFFRACTION	f_plane_restr	0.01	1182

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 (%)
2.2058-2.2508	0.3243	117	0.2593	2529	X-RAY DIFFRACTION	93
2.2508-2.2998	0.3272	141	0.264	2729	X-RAY DIFFRACTION	100
2.2998-2.3533	0.3269	160	0.2621	2699	X-RAY DIFFRACTION	100
2.3533-2.4121	0.3011	129	0.2689	2700	X-RAY DIFFRACTION	100
2.4121-2.4773	0.316	154	0.262	2720	X-RAY DIFFRACTION	100
2.4773-2.5502	0.319	154	0.2598	2701	X-RAY DIFFRACTION	100
2.5502-2.6325	0.3525	146	0.257	2697	X-RAY DIFFRACTION	100
2.6325-2.7266	0.3222	142	0.2489	2721	X-RAY DIFFRACTION	100
2.7266-2.8358	0.271	150	0.2443	2707	X-RAY DIFFRACTION	100
2.8358-2.9648	0.2709	119	0.2437	2748	X-RAY DIFFRACTION	100
2.9648-3.1211	0.3179	130	0.232	2700	X-RAY DIFFRACTION	100
3.1211-3.3165	0.2639	157	0.2195	2702	X-RAY DIFFRACTION	100
3.3165-3.5725	0.2325	127	0.2074	2735	X-RAY DIFFRACTION	100
3.5725-3.9318	0.2478	142	0.1954	2736	X-RAY DIFFRACTION	100
3.9318-4.5003	0.2343	122	0.1772	2748	X-RAY DIFFRACTION	99
4.5003-5.6681	0.2019	149	0.1737	2711	X-RAY DIFFRACTION	99
5.6681-44.3649	0.2381	140	0.2095	2752	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	1.7493	0.4254	-0.9077	1.8733	-0.416	4.1271	-0.0585	0.0264	-0.2768	-0.1149	0.015	-0.4185	0.0069	0.3054	-0.0634	0.2033	-0.011	0.0377	0.2617	0.0058	0.4503	28.0853	-12.5854	29.7726
2	4.003	-1.4591	1.5731	4.2917	-2.7429	7.2344	0.1014	-0.0728	-0.2837	-0.3542	-0.235	-0.7015	0.1745	0.1443	-0.0027	0.2694	0.0428	0.0099	0.2646	0.0098	0.4672	33.4577	-16.3232	27.7259
3	2.8395	0.2497	-0.0089	4.509	-0.8145	0.4293	0.2816	0.2271	0.2577	-0.6131	0.2421	0.0043	-0.3263	-0.1079	-0.3701	0.3878	0.0157	-0.0149	0.2659	-0.0229	0.2696	26.2349	-7.4129	25.2526
4	4.9714	-0.175	-1.2147	1.0888	0.7725	4.037	-0.1987	-0.3393	0.1409	0.4086	0.0511	0.8924	0.1447	-0.1475	-0.0971	0.301	0.0293	0.0271	0.3661	-0.0083	0.3697	26.7477	-16.7305	41.9308
5	0.1895	-0.8191	0.1549	3.7093	-0.719	0.1312	-0.0336	0.2402	-0.2478	0.1143	0.3235	0.4285	0.2496	-0.5438	-0.1399	0.3418	-0.1148	-0.0284	0.3911	-0.0272	0.4136	31.3144	7.3059	24.2616
6	2.3993	-0.9581	-0.7093	4.2541	1.0205	2.1346	-0.2173	-0.1493	0.0158	0.4217	0.0165	0.3237	0.1474	0.0905	0.2711	0.1463	-0.0051	-0.0538	0.1937	0.0216	0.2464	25.5433	21.3265	35.9249
7	1.4883	-0.6936	-0.7797	4.3675	0.6916	1.279	-0.1208	-0.2678	0.3491	0.4587	0.1753	-0.345	-0.0262	0.2572	-0.0195	0.2347	0.0258	-0.1248	0.2716	-0.0275	0.3086	29.0432	29.7752	39.6719
8	1.9041	-0.398	0.2112	4.2675	0.2986	1.8433	-0.0708	-0.2793	-0.2097	0.4608	0.2088	0.23	-0.142	-0.1064	-0.0207	0.2754	0.0622	0.0093	0.2806	0.0839	0.3055	10.3846	-13.6062	44.5444
9	0.4312	0.0269	0.0865	4.4362	-0.25	0.2882	-0.0589	-0.0045	0.0966	0.216	0.114	0.2732	-0.0805	-0.0039	-0.0449	0.1662	-0.0001	-0.0352	0.2677	0.0268	0.3213	12.0998	13.1923	36.0638
10	2.0971	-0.0393	-0.6761	3.3903	-0.8283	3.1133	-0.0199	-0.1485	0.2504	0.2791	-0.0427	-0.0721	-0.2866	0.2525	0.1659	0.4362	-0.0561	0.0453	0.3421	0.0255	0.2864	38.0514	48.0181	9.8509
11	8.0842	3.7281	0.1112	3.9315	-0.3044	3.1707	0.3426	-0.6488	0.3623	0.4746	-0.2009	-0.3443	-0.5102	1.1062	0.1969	0.5237	-0.1523	0.0461	0.488	-0.082	0.3483	38.8332	51.8698	15.568
12	1.9425	2.0941	-0.1777	3.5414	-0.9715	2.4325	-0.0799	0.0352	-0.0162	-0.0879	0.0977	0.2701	0.2727	-0.1892	-0.0988	0.3922	-0.0382	0.0959	0.4118	0.0392	0.3918	33.3549	42.6835	10.4011
13	4.2501	-0.2943	0.0787	0.3484	-0.228	4.8008	0.3419	-0.0663	0.8551	-0.7196	0.5525	0.3606	-0.7052	0.2605	0.1348	0.6614	-0.1661	0.1985	0.3949	0.036	0.518	47.6276	52.3348	2.721
14	-0.0123	0.0221	-0.0198	3.2717	-0.1717	-0.0182	-0.0006	0.3305	0.2626	-0.2007	0.0547	-0.1667	-0.3827	-0.2328	-0.0263	0.4161	-0.0458	0.0417	0.2913	0.0444	0.5248	35.4648	27.9483	15.5026
15	3.0549	-0.0893	-1.0846	2.7824	1.3803	3.4609	0.1986	0.2651	-0.025	-0.5295	-0.1058	-0.3924	-0.0604	0.039	-0.0017	0.3495	-0.1003	0.0271	0.2317	-0.0046	0.3068	43.6339	14.013	5.1242
16	1.9503	-1.2064	0.247	2.1171	-1.1874	0.8903	-0.1388	0.1005	-0.3717	-0.4608	-0.0939	-0.3632	0.3481	0.2528	-0.2317	0.3894	-0.0628	0.1345	0.3108	-0.0826	0.5147	49.1741	5.8816	6.5816
17	2.6158	-0.9611	-0.7851	4.6721	-0.1484	2.7126	0.0029	0.2478	-0.0509	-0.0945	-0.1581	-0.1047	0.0952	0.0227	0.086	0.3182	-0.0098	0.0523	0.3236	0.0588	0.2824	42.6047	47.8117	-13.4113
18	0.1943	0.5	-0.5889	4.581	-1.3232	1.1568	-0.1904	0.2872	-0.091	-0.8974	0.2198	0.0688	0.4794	-0.2891	-0.0861	0.489	-0.1299	-0.0139	0.4578	-0.009	0.3476	35.4412	18.8973	-5.5186

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 76 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 91 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 102 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 103 through 114 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 115 through 175 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 176 through 215 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 76 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 77 through 218 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 62 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 63 through 76 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 77 through 91 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 92 through 102 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 103 through 114 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 115 through 175 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 176 through 215 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 91 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 92 through 218 )

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