PDB-6s3d: Structure of D25 Fab in complex with scaffold S0_2.126

ID or keywords:

Entry

Database: PDB / ID: 6s3d

Title

Structure of D25 Fab in complex with scaffold S0_2.126

Components

Heavy Chain
Light Chain
S0_2.126

Keywords

ANTIVIRAL PROTEIN / hRSV / D25 / Fab fragment

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Cramer, J.T. / Krey, T.

Funding support

Germany, 1items

Citation

Journal: Science / Year: 2020
Title: De novo protein design enables the precise induction of RSV-neutralizing antibodies.
Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. ...

History

Deposition	Jun 25, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2020	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	May 27, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Jan 24, 2024	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 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6s3d.cif.gz	745.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6s3d.ent.gz	623.3 KB	Display	PDB format
PDBx/mmJSON format	6s3d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6s3d_validation.pdf.gz	517 KB	Display	wwPDB validaton report
Full document	6s3d_full_validation.pdf.gz	538.8 KB	Display
Data in XML	6s3d_validation.xml.gz	64.1 KB	Display
Data in CIF	6s3d_validation.cif.gz	86.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3d ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3d	HTTPS FTP

-
Related structure data

Related structure data	6vtwC 6xwiC 6xxvC 4jhaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3qwo-2 5epm-1 3qwo-1 6was-2 5kn5-2 5kn5-1 5u3m-d 6snd-1 3kr3-d 6z7w-3 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)

-
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: Heavy Chain

B: Light Chain

C: Heavy Chain

D: Light Chain

E: Heavy Chain

F: Light Chain

H: Heavy Chain

L: Light Chain

M: S0_2.126

N: S0_2.126

O: S0_2.126

P: S0_2.126

235 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Heavy Chain

B: Light Chain

N: S0_2.126

defined by author&software
Evidence: gel filtration
58.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Heavy Chain

D: Light Chain

M: S0_2.126

defined by author&software
58.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Heavy Chain

F: Light Chain

O: S0_2.126

defined by author&software
58.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

H: Heavy Chain

L: Light Chain

P: S0_2.126

defined by author&software
58.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.272, 126.977, 156.091
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Heavy Chain Mass: 25749.963 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	Light Chain Mass: 24700.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein	S0_2.126 Mass: 8209.471 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.05 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% (w/v) PEG 8000, 100 mM HEPES pH 7.5, 200 mM Calcium acetate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-3 / Wavelength: 0.9677 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 27, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9677 Å / Relative weight: 1

Reflection

Resolution: 3→49.086 Å / Num. obs: 96992 / % possible obs: 99.7 % / Redundancy: 7.238 % / B_iso Wilson estimate: 65.981 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.156 / R_rim(I) all: 0.168 / Χ²: 1.09 / Net I/σ(I): 8.69

Reflection shell

Resolution (Å)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	Diffraction-ID	% possible all
3-3.08	1.38	7183	0.81	1	99.3
3.08-3.16		6971		1
3.16-3.25		6872		1
3.25-3.35		6418		1
3.35-3.46		6418		1
3.46-3.58		6202		1
3.58-3.72		6033		1
3.72-3.87		5733		1
3.87-4.04		5510		1
4.04-4.24		5249		1
4.24-4.47		4900		1
4.47-4.74		4760		1
4.74-5.07		4488		1
5.07-5.47		4139		1
5.47-5.99		3831		1
5.99-6.7		3031		1
6.7-7.74		3031		1
7.74-9.48		2599		1
9.48-13.41		1982		1
13.41-49.086	28.98	1048		1	96.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS	BUILT=20190315	data reduction
XSCALE	BUILT=20190315	data scaling
PHASER	2.8.1	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4jha

4jha

Resolution: 3→49.086 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.01

	R_factor	Num. reflection	% reflection
R_free	0.2917	2515	5 %
R_work	0.269	-	-
obs	0.2702	50267	98.76 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→49.086 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14439	0	0	0	14439

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	14762
X-RAY DIFFRACTION	f_angle_d	0.793	20129
X-RAY DIFFRACTION	f_dihedral_angle_d	4.042	8837
X-RAY DIFFRACTION	f_chiral_restr	0.05	2338
X-RAY DIFFRACTION	f_plane_restr	0.006	2575

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 (%)
3-3.0577	0.4448	138	0.3963	2611	X-RAY DIFFRACTION	99
3.0577-3.1201	0.3721	138	0.3631	2617	X-RAY DIFFRACTION	99
3.1201-3.188	0.3767	139	0.3402	2649	X-RAY DIFFRACTION	99
3.188-3.2621	0.3996	138	0.3323	2639	X-RAY DIFFRACTION	100
3.2621-3.3437	0.339	140	0.3206	2638	X-RAY DIFFRACTION	99
3.3437-3.4341	0.3677	138	0.3173	2646	X-RAY DIFFRACTION	100
3.4341-3.5351	0.3619	140	0.2973	2646	X-RAY DIFFRACTION	100
3.5351-3.6491	0.3582	140	0.2785	2663	X-RAY DIFFRACTION	100
3.6491-3.7795	0.2876	139	0.2741	2627	X-RAY DIFFRACTION	99
3.7795-3.9308	0.3424	140	0.2784	2667	X-RAY DIFFRACTION	100
3.9308-4.1096	0.3146	140	0.27	2682	X-RAY DIFFRACTION	100
4.1096-4.3262	0.2461	138	0.2468	2598	X-RAY DIFFRACTION	97
4.3262-4.597	0.261	138	0.22	2632	X-RAY DIFFRACTION	98
4.597-4.9516	0.1933	141	0.2159	2688	X-RAY DIFFRACTION	100
4.9516-5.4494	0.2543	142	0.2421	2706	X-RAY DIFFRACTION	100
5.4494-6.2365	0.3333	143	0.2534	2713	X-RAY DIFFRACTION	100
6.2365-7.8522	0.287	146	0.2815	2754	X-RAY DIFFRACTION	100
7.8522-49.0921	0.2325	137	0.2512	2576	X-RAY DIFFRACTION	90

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	3.5245	-1.9878	-1.7996	4.2437	1.6583	2.3918	-0.7074	-0.7553	-0.8437	1.4789	0.3815	0.8527	1.1291	-0.0607	0.3219	0.8167	0.0355	0.4447	0.6441	0.2886	0.8851	-25.4056	-14.9363	5.0415
2	3.3416	-1.7972	-1.8436	4.6084	2.5411	3.1814	-0.2706	-0.3823	-0.1289	0.1288	0.0168	0.975	0.1889	-0.0732	0.2373	0.6473	0.0873	-0.083	0.3912	0.1056	1.1259	-32.4079	2.5789	-0.0149
3	4.3007	2.5478	-0.4283	3.9375	-2.3928	2.2825	0.153	-1.6888	-1.3296	0.443	-0.3948	-1.1957	0.4592	0.3313	0.262	1.1003	0.0218	-0.0989	0.9589	0.7207	0.9553	14.9858	-26.3056	4.9966
4	4.1337	1.8623	-0.0356	2.4427	-0.7761	2.4368	-0.123	-0.6659	-1.6126	0.0797	-0.3882	0.0524	0.3568	-0.1149	0.3635	0.6579	-0.0205	0.1759	0.4858	0.3905	0.8568	-2.3695	-32.8363	-0.7973
5	5.8969	3.6353	2.633	7.1875	2.8822	3.8129	0.5138	-1.4631	1.2681	1.3672	-1.005	1.0975	0.3304	-0.5821	0.5188	0.7414	-0.1666	0.2498	0.7744	-0.1192	0.937	-14.8455	26.2049	4.9147
6	6.4569	0.8965	2.5411	4.9419	0.4121	2.0172	-0.0902	-0.5051	1.3884	0.6893	-0.1737	0.5006	0.0814	0.1387	0.2948	0.8484	0.0055	0.0444	0.426	0.1	0.895	2.5583	32.846	-0.9786
7	3.9791	-3.0083	2.4754	6.2371	-2.3192	2.3101	-0.965	-1.5145	1.2867	1.4629	0.9724	-2.4358	0.2478	-0.2535	0.066	1.661	0.3702	-0.1672	0.809	0.1361	0.7291	25.5314	14.9791	5.0854
8	1.934	-1.3143	-0.2079	3.7628	-0.1334	1.5026	-0.0944	-0.2369	-0.6972	0.8483	0.2234	-1.6678	0.5308	0.004	-0.0312	1.0269	-0.0647	-0.6409	0.5491	0.5196	0.9548	32.5402	-2.5315	0.1329
9	7.7408	-1.0124	0.5849	3.6908	1.3883	9.3524	-0.2774	2.5091	-0.4204	-1.3427	-0.1197	-2.1521	-0.3104	1.0496	0.1896	1.0853	-0.1891	0.7252	1.2133	-0.0533	1.4989	26.523	-20.7525	-30.1709
10	6.8372	0.8788	-0.1793	8.7813	0.3504	6.4298	0.2466	1.3864	-1.3101	-2.4377	0.2409	0.5578	0.5913	-0.2052	-0.3335	1.6016	0.0435	-0.2776	0.8712	-0.3525	0.9887	-21.2786	-26.393	-29.8252
11	6.1394	-1.7693	2.6781	7.2146	0.031	8.1998	-0.3359	1.4685	0.8217	-1.6739	-0.1652	0.4076	-0.9884	-0.476	0.3545	1.0934	-0.13	-0.2954	1.2006	0.3505	1.0974	-26.7782	20.9471	-30.003
12	3.1324	0.3107	0.6576	6.5908	-2.2479	7.5076	-0.3205	1.0306	0.5993	-2.5594	0.3821	-0.4114	-1.3977	0.1107	-0.2282	1.6618	0.2376	0.3148	0.8664	0.4341	1.1485	21.5851	26.3953	-29.9269

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 4 through 224)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 3 through 213)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 4 through 228)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 2 through 213)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 4 through 228)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 3 through 213)
7	X-RAY DIFFRACTION	7	(chain 'H' and resid 4 through 222)
8	X-RAY DIFFRACTION	8	(chain 'L' and resid 3 through 213)
9	X-RAY DIFFRACTION	9	(chain 'M' and resid 2 through 60)
10	X-RAY DIFFRACTION	10	(chain 'N' and resid 2 through 59)
11	X-RAY DIFFRACTION	11	(chain 'O' and resid 2 through 60)
12	X-RAY DIFFRACTION	12	(chain 'P' and resid 2 through 59)

-
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