PDB-5wcc: Crystal structure of the broadly neutralizing Influenza A antibod...

ID or keywords:

Entry

Database: PDB / ID: 5wcc

Title

Crystal structure of the broadly neutralizing Influenza A antibody VRC 315 02-1F07 Fab.

Components

(VRC 315 02-1F07 Fab ...) x 2

Keywords

IMMUNE SYSTEM / antibody / influenza / human vaccine trial

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: 2.461 Å

Authors

Joyce, M.G. / Andrews, S.F. / Mascola, J.R. / McDermott, A.B. / Kwong, P.D.

Citation

Journal: Sci Immunol / Year: 2017
Title: Preferential induction of cross-group influenza A hemagglutinin stem-specific memory B cells after H7N9 immunization in humans.
Authors: Andrews, S.F. / Joyce, M.G. / Chambers, M.J. / Gillespie, R.A. / Kanekiyo, M. / Leung, K. / Yang, E.S. / Tsybovsky, Y. / Wheatley, A.K. / Crank, M.C. / Boyington, J.C. / Prabhakaran, M.S. / ...

History

Deposition	Jun 29, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2	Oct 4, 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 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5wcc.cif.gz	354.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5wcc.ent.gz	286.5 KB	Display	PDB format
PDBx/mmJSON format	5wcc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5wcc_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5wcc_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5wcc_validation.xml.gz	36.2 KB	Display
Data in CIF	5wcc_validation.cif.gz	50.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wc/5wcc ftp://data.pdbj.org/pub/pdb/validation_reports/wc/5wcc	HTTPS FTP

-
Related structure data

Related structure data	5ty6SC 5u4rC 5wcaC 5wcdC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1uz8-1 4qhm-1 1mcq-d 3tnn-3 3lrs-1 6pzh-1 4d9l-3 5cgy-1 5jo5-3 5f88-1 2gfb-2 5mtl-2 5jo5-4 5t78-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
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: VRC 315 02-1F07 Fab Heavy chain

L: VRC 315 02-1F07 Fab Light chain

A: VRC 315 02-1F07 Fab Heavy chain

B: VRC 315 02-1F07 Fab Light chain

hetero molecules

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

1

H: VRC 315 02-1F07 Fab Heavy chain

L: VRC 315 02-1F07 Fab Light chain

hetero molecules

defined by author&software
Evidence: gel filtration, Heavy and light chain form a dimer.
49.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: VRC 315 02-1F07 Fab Heavy chain

B: VRC 315 02-1F07 Fab Light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	179.217, 70.581, 94.543
Angle α, β, γ (deg.)	90.00, 111.86, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	L-487- HOH
2	1	B-492- HOH

-
Antibody , 2 types, 4 molecules HALB

#1: Antibody	VRC 315 02-1F07 Fab Heavy chain Mass: 24275.232 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	VRC 315 02-1F07 Fab Light chain Mass: 23190.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 306 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 Mass: 1529.829 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆₉H₁₄₀O₃₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58.02 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 40% (w/v) PEG-400, 11% (w/v) PEG-8000, 0.1 M Tris, pH 8.8

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.45→46.624 Å / Num. obs: 39756 / % possible obs: 100 % / Redundancy: 5.9 % / R_merge(I) obs: 0.161 / Net I/σ(I): 11.56
Reflection shell	Resolution: 2.45→2.54 Å / R_merge(I) obs: 0.861

-
Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5TY6

5ty6

Resolution: 2.461→46.624 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2404	1996	5.02 %
R_work	0.2029	-	-
obs	0.2048	39748	99.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.461→46.624 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6514	0	69	297	6880

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6742
X-RAY DIFFRACTION	f_angle_d	0.586	9183
X-RAY DIFFRACTION	f_dihedral_angle_d	14.52	4015
X-RAY DIFFRACTION	f_chiral_restr	0.043	1034
X-RAY DIFFRACTION	f_plane_restr	0.005	1162

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 (%)
2.4615-2.523	0.3142	136	0.2721	2481	X-RAY DIFFRACTION	92
2.523-2.5912	0.2795	131	0.2525	2682	X-RAY DIFFRACTION	100
2.5912-2.6675	0.2789	142	0.2518	2676	X-RAY DIFFRACTION	100
2.6675-2.7536	0.3089	130	0.2441	2720	X-RAY DIFFRACTION	100
2.7536-2.852	0.2644	143	0.2386	2706	X-RAY DIFFRACTION	100
2.852-2.9661	0.2583	150	0.2218	2678	X-RAY DIFFRACTION	100
2.9661-3.1011	0.2478	132	0.2304	2721	X-RAY DIFFRACTION	100
3.1011-3.2645	0.2768	126	0.2237	2725	X-RAY DIFFRACTION	100
3.2645-3.469	0.244	160	0.205	2691	X-RAY DIFFRACTION	100
3.469-3.7368	0.221	148	0.1895	2704	X-RAY DIFFRACTION	100
3.7368-4.1126	0.2229	152	0.184	2701	X-RAY DIFFRACTION	100
4.1126-4.7072	0.203	144	0.1578	2733	X-RAY DIFFRACTION	100
4.7072-5.9287	0.1872	140	0.1795	2745	X-RAY DIFFRACTION	100
5.9287-46.6324	0.2724	162	0.2088	2789	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	1.5416	-0.505	0.1669	2.12	-0.4607	0.9405	0.1188	0.1439	-0.3448	-0.0496	0.0019	-0.1111	0.2411	0.4621	0.0174	0.292	0.0934	0.0418	0.4487	-0.0471	0.3064	172.8172	-0.9424	88.2179
2	1.7132	-0.0539	0.0437	0.9196	-0.2082	0.7848	-0.2869	-0.1843	-0.1654	0.0311	0.0691	-0.0245	0.3332	0.3025	-0.7031	0.2215	-0.0011	-0.1009	0.0414	-0.0264	0.1969	161.7515	4.9426	97.0478
3	3.3908	-0.7556	-0.5421	4.7482	0.691	3.3034	-0.2325	-0.2569	-0.1547	-0.0533	0.0217	0.0573	0.2945	-0.0498	0.1393	0.3965	-0.0154	0.0113	0.2065	0.0468	0.3262	140.5454	-1.7288	109.5183
4	0.8542	-0.1582	0.5738	0.2835	-0.1418	0.3928	-0.3096	-0.0038	0.8998	0.4305	0.0618	-0.425	-0.0476	0.0306	-0.0108	0.3785	-0.0192	-0.0708	0.3066	-0.0425	0.3338	161.1812	24.4832	95.1521
5	0.3607	-0.5006	-0.1395	0.7334	0.147	0.1514	0.1629	0.1308	0.0405	-0.1469	-0.2778	-0.0897	-0.0303	0.4068	-0.1142	0.3476	-0.0689	0.0562	0.5018	0.022	0.2914	166.7104	16.6455	88.04
6	0.8381	-0.6491	-0.786	1.12	0.3277	1.3197	0.0346	0.2748	0.3471	0.092	0.0141	-0.1793	-0.3161	0.4982	-0.0009	0.2643	-0.1307	-0.0218	0.3137	0.0256	0.3809	166.8898	20.7793	88.6501
7	1.2455	-0.4182	0.6312	2.3414	-1.58	3.7342	-0.0116	-0.1935	-0.1596	0.1364	0.01	-0.1841	0.0375	0.0722	-0.0393	0.312	0.0205	-0.0253	0.2188	0.0068	0.327	151.7946	10.0977	111.9021
8	5.2967	-1.4332	3.334	3.5295	1.8572	4.4701	0.1406	-0.5661	-0.3079	1.0139	0.2809	0.2538	-0.1979	-0.321	-0.1435	0.338	0.052	-0.0033	0.3096	0.0338	0.3243	150.407	14.8518	120.0194
9	1.5833	0.439	0.8453	2.3037	-0.6353	1.5303	0.0027	-0.3263	0.3026	0.1055	-0.2678	-0.0649	-0.1837	0.2813	0	0.3478	-0.0628	-0.0454	0.4767	-0.0346	0.2836	147.298	-24.4673	151.2946
10	1.2687	-0.0444	0.5275	0.484	1.1581	2.9344	-0.0763	-0.3883	0.1619	0.1404	-0.3694	-0.5365	-1.4444	0.2116	-0.5701	0.0358	-0.032	-0.0528	0.1085	-0.0206	0.189	143.6325	-25.2473	142.4176
11	2.6637	-0.2234	-0.8087	4.304	-0.5668	2.4403	0.0929	0.2291	-0.0039	-0.0355	-0.0669	0.0036	-0.1592	0.18	0.0208	0.3743	-0.0117	0.0303	0.2218	0.0363	0.3613	139.9126	-25.0021	112.6421
12	0.7386	-0.2732	0.6614	0.1614	-0.335	0.94	0.0626	0.4031	0.0561	-0.0934	-0.1021	-0.1022	0.794	0.6753	-0.1765	0.3543	0.1122	0.1113	0.3099	0.0168	0.4191	141.6361	-49.9654	136.2575
13	0.459	0.2979	0.2179	0.4693	0.2395	0.5193	0.1419	0.2402	-0.5185	0.3911	0.2184	-0.6452	0.6793	0.8008	0.2605	0.5101	0.216	-0.0885	0.608	0.0756	0.7653	153.346	-49.4804	148.0159
14	0.7431	0.2654	-0.9513	1.4169	0.2884	1.2445	-0.018	-0.5722	-0.0928	0.2056	-0.0345	-0.1238	0.2313	0.1899	-0.021	0.2968	0.0676	-0.0695	0.345	0.0725	0.2902	142.5996	-44.7883	146.7231
15	2.7176	1.1951	-1.9047	0.8419	-1.3942	2.2432	-0.0396	0.0544	0.1446	-0.0419	0.0027	-0.0876	-0.1543	0.1257	0.0039	0.3025	-0.0292	0.0039	0.1782	-0.011	0.3258	146.2442	-36.1834	120.4737
16	4.6752	1.7985	-2.3682	5.9967	-2.5253	4.5066	-0.3165	0.1611	-0.058	-0.6134	-0.0781	-0.9719	0.1271	0.5366	0.2636	0.3396	-0.0467	-0.0118	0.3461	0.0279	0.4604	156.7231	-36.6244	114.6204

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 95 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 96 through 134 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 135 through 216 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 2 through 25 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 26 through 48 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 49 through 101 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 102 through 197 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 198 through 211 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1 through 95 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 96 through 119 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 120 through 216 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 3 through 18 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 19 through 32 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 33 through 101 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 102 through 180 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 181 through 211 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 2 types, 4 molecules HALB

-
Non-polymers , 4 types, 306 molecules

-
Details

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Antibody , 2 types, 4 molecules HALB

-Non-polymers , 4 types, 306 molecules

-Details

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 2 types, 4 molecules HALB

-
Non-polymers , 4 types, 306 molecules

-
Details

-
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