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

ID or keywords:

Entry

Database: PDB / ID: 5wcd

Title

Crystal structure of the broadly neutralizing Influenza A antibody VRC 315 04-1D02 Fab.

Components

VRC315 04-1D02 Fab Heavy chain
VRC315 04-1D02 Fab Light chain

Keywords

IMMUNE SYSTEM /

antibody /

influenza /

human vaccine trial

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta /

PHOSPHATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.814 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	Aug 23, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5wcd.cif.gz	249.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5wcd.ent.gz	214.1 KB	Display	PDB format
PDBx/mmJSON format	5wcd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wc/5wcd ftp://data.pdbj.org/pub/pdb/validation_reports/wc/5wcd	HTTPS FTP

-
Related structure data

Related structure data	5ty6C 5u4rC 5wcaC 5wccC C: citing same article (ref.)
Similar structure data	5dq9-1 3pho-d 1bbd-d 6elj-1 2gk0-1 2eh8-d 6qna-3 4yho-d 6cdp-d 4ojf-d 2gfb-4 1u6a-d 1mh5-1 6tcp-1 3bz4-3 6cdm-2 6ele-2 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: VRC315 04-1D02 Fab Heavy chain

L: VRC315 04-1D02 Fab Light chain

hetero molecules

47.7 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, Asymmetric unit contains one biological dimer.

Unit cell

Length a, b, c (Å)	62.490, 77.683, 80.612
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	VRC315 04-1D02 Fab Heavy chain Mass: 24453.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	VRC315 04-1D02 Fab Light chain Mass: 22977.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG-1500

-
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: 1.81→34.991 Å / Num. obs: 33529 / % possible obs: 92.6 % / Redundancy: 6.1 % / Net I/σ(I): 16.14

-
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: 1.814→34.991 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.14

	R_factor	Num. reflection	% reflection
R_free	0.2161	1669	4.99 %
R_work	0.1771	-	-
obs	0.1791	33464	92.42 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.814→34.991 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3214	0	15	240	3469

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3327
X-RAY DIFFRACTION	f_angle_d	0.701	4547
X-RAY DIFFRACTION	f_dihedral_angle_d	17.243	1968
X-RAY DIFFRACTION	f_chiral_restr	0.048	515
X-RAY DIFFRACTION	f_plane_restr	0.004	577

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 (%)
1.8142-1.8676	0.306	93	0.2907	1685	X-RAY DIFFRACTION	60
1.8676-1.9278	0.2992	92	0.2778	2075	X-RAY DIFFRACTION	73
1.9278-1.9967	0.3181	120	0.2654	2352	X-RAY DIFFRACTION	83
1.9967-2.0767	0.2911	165	0.2476	2617	X-RAY DIFFRACTION	94
2.0767-2.1712	0.2503	144	0.221	2800	X-RAY DIFFRACTION	99
2.1712-2.2856	0.2412	144	0.2011	2838	X-RAY DIFFRACTION	100
2.2856-2.4288	0.2559	163	0.194	2849	X-RAY DIFFRACTION	100
2.4288-2.6163	0.2316	139	0.1876	2872	X-RAY DIFFRACTION	100
2.6163-2.8794	0.2272	135	0.1896	2867	X-RAY DIFFRACTION	100
2.8794-3.2958	0.2029	156	0.1686	2882	X-RAY DIFFRACTION	100
3.2958-4.1513	0.2033	157	0.1456	2918	X-RAY DIFFRACTION	100
4.1513-34.9979	0.1772	161	0.1559	3040	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	6.0589	-2.91	2.5128	3.8747	-0.4486	2.5023	-0.4526	0.2257	0.8226	-0.0988	0.002	-0.2852	-0.5359	0.0645	0.468	0.3385	-0.0277	0.0068	0.2326	0.0467	0.2156	17.414	18.6051	69.0738
2	4.3675	-2.5605	0.8085	1.935	0.0521	0.7711	-0.0872	0.0043	0.1823	-0.0538	-0.0216	-0.0567	-0.0558	0.0729	0.0824	0.2535	-0.0196	-0.0026	0.2488	-0.0072	0.1917	22.552	9.2989	71.5754
3	2.5482	-2.3419	-2.3153	4.975	4.0785	3.9652	0.1166	0.0524	-0.14	-0.1093	-0.1774	0.3534	-0.3673	-0.4276	0.2434	0.2578	-0.0007	0.0051	0.3148	-0.0366	0.2401	10.6976	8.634	76.6539
4	5.5332	-5.2347	-1.0783	5.9401	0.5516	3.6267	0.0054	-0.0962	-0.2733	-0.3852	-0.0383	0.5146	0.1188	-0.0297	-0.1023	0.3159	-0.0589	-0.0399	0.2617	-0.022	0.319	12.9258	1.1841	67.2599
5	9.0212	-3.407	0.3678	3.6995	0.3145	1.7056	0.0876	0.7574	-0.0789	-0.282	-0.2741	0.138	-0.1574	0.0066	0.1013	0.3157	0.0025	-0.0243	0.2816	-0.0109	0.2472	15.7853	10.9878	64.9915
6	4.0019	-3.6229	1.695	4.6775	-1.2444	3.8225	-0.0419	-0.0166	-0.1905	-0.187	0.1309	-0.0122	0.3871	0.2513	0.0113	0.3232	-0.0264	0.0023	0.2835	-0.0029	0.3061	22.791	0.8924	76.8552
7	1.8549	-2.6214	0.5059	4.1276	-1.007	0.2518	0.0089	0.1704	-0.056	0.028	-0.07	0.1167	-0.1257	0.0339	0.028	0.3024	-0.0213	-0.0337	0.2419	0.0004	0.2314	13.8093	18.4671	73.9911
8	7.5373	1.2551	4.1677	4.2828	1.0678	2.9723	0.0487	-0.0911	0.4171	0.0598	-0.184	-0.2876	-0.2294	0.1707	0.0403	0.2678	-0.0448	0.024	0.3627	0.0248	0.2436	18.1073	37.8531	80.0343
9	2.6092	0.3097	0.221	2.9729	0.938	2.6414	0.2387	-0.5194	0.1563	0.1205	-0.0097	-0.4273	0.0033	0.3688	-0.0722	0.2281	-0.055	-0.0061	0.3384	0.0071	0.2709	15.0212	33.9651	83.9714
10	1.0777	-0.8684	0.3776	1.6275	-0.6756	3.2134	-0.0665	-0.5161	0.3815	0.4281	0.0612	-0.7915	-0.4808	0.7001	0.1572	0.2981	-0.0712	-0.0831	0.5394	-0.1176	0.5692	25.2762	40.5873	86.3092
11	6.8956	5.4977	5.5154	6.3187	4.8166	4.5167	-0.1452	0.2161	-0.3115	-0.2225	0.3214	-0.5406	-0.2638	0.5966	-0.0853	0.3256	-0.0741	0.0387	0.3918	0.0031	0.2917	21.3679	36.627	73.6316
12	5.9402	0.1454	0.757	5.8828	0.2775	5.9074	-0.1601	-0.3409	-0.0125	0.433	0.1445	0.3366	-0.7976	-0.9673	0.1653	0.3281	0.0549	0.1007	0.3331	0.0785	0.2515	9.8803	8.48	98.5947
13	4.5597	1.4573	-1.7531	5.3279	-1.7843	4.3117	-0.1755	0.0775	-0.4121	-0.1719	0.1323	0.144	-0.0136	-0.0692	0.0149	0.2843	0.0226	0.0086	0.2925	0.024	0.2666	14.4329	2.8313	88.7259
14	7.0418	2.6106	-2.6481	6.2465	-0.9381	1.4394	0.0014	-0.7927	-0.1214	-0.0281	-0.1093	-0.4295	-0.1822	0.5917	0.033	0.2776	0.0016	-0.0219	0.4306	0.0208	0.2921	25.2762	1.4866	92.4718
15	3.1357	0.2834	1.3365	2.5284	0.8904	6.0887	-0.072	-0.2557	-0.1651	0.2386	0.1437	0.1201	-0.2608	-0.1282	-0.0784	0.2937	0.0175	0.0271	0.3738	0.0492	0.2955	15.6605	4.9845	94.4848
16	3.206	1.8355	0.2846	7.7758	1.1231	1.8936	-0.1284	0.4807	-0.8774	-0.6127	0.2475	-0.3313	0.3728	-0.5414	0.2062	0.4343	-0.074	-0.0342	0.4097	-0.0353	0.4184	10.235	-0.9768	79.2491
17	0.2698	0.4405	-0.3501	8.7297	-1.2809	0.4622	-0.1254	-0.1473	-0.0682	1.0734	0.0346	-0.439	-0.0971	0.2622	-0.0378	0.4595	0.0468	-0.0724	0.3456	-0.014	0.2842	14.9467	27.8314	99.7347
18	2.2395	0.7167	-0.0488	5.7772	-2.5145	5.7384	-0.0649	0.0672	0.1903	-0.3635	-0.01	-0.2663	-0.1405	-0.0181	-0.0217	0.2457	-0.0479	-0.0368	0.2714	-0.047	0.2962	12.2594	43.3001	89.2585
19	3.4696	2.236	-0.0493	2.9368	-0.9142	5.2792	0.169	-0.1329	-0.0857	-0.011	-0.2571	-0.351	0.1253	-0.147	0.0696	0.2618	-0.0158	-0.0288	0.3759	-0.0356	0.3252	9.4563	36.2797	93.8654
20	1.7261	2.7211	-0.4309	4.3672	-0.6712	5.6545	0.0225	-0.225	0.3493	0.2172	-0.075	0.468	-0.8634	0.1242	0.1473	0.368	0.0086	-0.0301	0.3175	-0.0534	0.3369	10.2682	48.626	93.5688

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 39 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 40 through 51 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 52 through 66 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 67 through 90 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 91 through 108 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 109 through 130 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 131 through 168 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 169 through 186 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 187 through 204 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 205 through 224 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 3 through 17 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 18 through 50 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 51 through 63 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 64 through 93 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 94 through 105 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 106 through 123 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 124 through 155 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 156 through 178 )
20	X-RAY DIFFRACTION	20	chain 'L' and (resid 179 through 214 )

-
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

-
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

-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

-
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