PDB-6w5d: Crystal Structure of Fab RSB1

ID or keywords:

Entry

Database: PDB / ID: 6w5d

Title

Crystal Structure of Fab RSB1

Components

RSB1 Fab Heavy Chain
RSB1 Fab Light Chain

Keywords

IMMUNE SYSTEM / RSV /

antibody / neutralization / prefusion /

vaccine

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Harshbarger, W. / Chandramouli, S. / Malito, M.

Citation

Journal: Plos Pathog. / Year: 2020
Title: Convergent structural features of respiratory syncytial virus neutralizing antibodies and plasticity of the site V epitope on prefusion F.
Authors: Harshbarger, W. / Tian, S. / Wahome, N. / Balsaraf, A. / Bhattacharya, D. / Jiang, D. / Pandey, R. / Tungare, K. / Friedrich, K. / Mehzabeen, N. / Biancucci, M. / Chinchilla-Olszar, D. / ...

History

Deposition	Mar 13, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6w5d.cif.gz	410.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6w5d.ent.gz	275.5 KB	Display	PDB format
PDBx/mmJSON format	6w5d.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/w5/6w5d ftp://data.pdbj.org/pub/pdb/validation_reports/w5/6w5d	HTTPS FTP

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Related structure data

Related structure data	6w52SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ggu-2 4jfx-1 3qhz-1 1dqq-2 2orb-2 5wca-d 4yx2-2 4r7n-8 5bk5-4 4qhk-1 4ouu-2 4trp-d 3qg7-d 3cfk-4 4a6y-2 6o3u-3 4xcy-4 4r7n-6 1ynl-d 1mcw-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)

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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) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1)

Deposited unit

H: RSB1 Fab Heavy Chain

L: RSB1 Fab Light Chain

A: RSB1 Fab Heavy Chain

B: RSB1 Fab Light Chain

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

1

H: RSB1 Fab Heavy Chain

L: RSB1 Fab Light Chain

defined by author&software
Evidence: gel filtration
55.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: RSB1 Fab Heavy Chain

B: RSB1 Fab Light Chain

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

Unit cell

Length a, b, c (Å)	70.360, 82.487, 75.965
Angle α, β, γ (deg.)	90.000, 94.893, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	ALA	ALA	chain 'A'	A	C	1 - 125	20 - 152
1	2	1	GLY	GLY	GLU	GLU	chain 'A'	A	C	134 - 212	161 - 239
2	3	1	GLN	GLN	ALA	ALA	(chain 'H' and (resid 1 through 126 or resid 134 through 213))	H	A	1 - 125	20 - 152
2	4	1	GLY	GLY	GLU	GLU	(chain 'H' and (resid 1 through 126 or resid 134 through 213))	H	A	134 - 212	161 - 239
1	5	2	GLN	GLN	SER	SER	chain 'B'	B	D	1 - 9	21 - 29
1	6	2	VAL	VAL	PRO	PRO	chain 'B'	B	D	11 - 208	30 - 232
2	7	2	GLN	GLN	SER	SER	chain 'L'	L	B	1 - 9	21 - 29
2	8	2	VAL	VAL	PRO	PRO	chain 'L'	L	B	11 - 208	30 - 232

NCS ensembles :

ID
1
2

#1: Antibody	RSB1 Fab Heavy Chain Mass: 29977.432 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	RSB1 Fab Light Chain Mass: 25137.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.41 Å³/Da / Density % sol: 48.99 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulfate, 0.1 M bis-tris pH 5.5, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→35.55 Å / Num. obs: 55626 / % possible obs: 89.09 % / Redundancy: 3.5 % / B_iso Wilson estimate: 24.41 Å² / CC_1/2: 0.84 / Net I/σ(I): 14.66
Reflection shell	Resolution: 2→2.07 Å / Num. unique obs: 4080 / CC_1/2: 0.748

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6W52

6w52

Resolution: 2→35.55 Å / SU ML: 0.2706 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.207

	R_factor	Num. reflection	% reflection
R_free	0.2772	1988	3.81 %
R_work	0.2322	-	-
obs	0.2339	52220	88.69 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.74 Å²

Refinement step

Cycle: LAST / Resolution: 2→35.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6401	0	0	583	6984

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0036	6556
X-RAY DIFFRACTION	f_angle_d	0.737	8954
X-RAY DIFFRACTION	f_chiral_restr	0.0527	1027
X-RAY DIFFRACTION	f_plane_restr	0.0056	1140
X-RAY DIFFRACTION	f_dihedral_angle_d	19.7184	918

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 (%)
2-2.05	0.2432	105	0.2293	2561	X-RAY DIFFRACTION	63.98
2.05-2.1	0.2988	102	0.2366	3104	X-RAY DIFFRACTION	76.79
2.1-2.16	0.3044	145	0.2416	3412	X-RAY DIFFRACTION	84.79
2.16-2.23	0.2972	168	0.2472	3599	X-RAY DIFFRACTION	89.86
2.23-2.31	0.3414	133	0.2495	3696	X-RAY DIFFRACTION	91.54
2.31-2.41	0.3122	146	0.2458	3677	X-RAY DIFFRACTION	91.46
2.41-2.51	0.3055	147	0.2533	3617	X-RAY DIFFRACTION	89.56
2.51-2.65	0.312	139	0.2532	3582	X-RAY DIFFRACTION	88.87
2.65-2.81	0.2859	144	0.2456	3928	X-RAY DIFFRACTION	96.58
2.81-3.03	0.2724	163	0.2378	3874	X-RAY DIFFRACTION	95.87
3.03-3.33	0.2704	160	0.2318	3840	X-RAY DIFFRACTION	95.6
3.33-3.82	0.2596	155	0.2252	3912	X-RAY DIFFRACTION	96.28
3.82-4.81	0.2443	129	0.2088	3489	X-RAY DIFFRACTION	85.27
4.81-35.55	0.2682	152	0.2238	3941	X-RAY DIFFRACTION	94.9

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	0.221229419012	0.211243103486	-0.037965538206	0.823347241978	0.192869341902	0.436403775545	0.038341084234	-0.0802981058201	-0.000507424298431	-0.122228600554	-0.00250716259085	0.0817941381958	0.0457650016772	0.266993091475	-0.00171080058695	0.253876527347	0.0465470222869	0.028573662436	0.19796271947	-0.0202627936442	0.134201564807	-31.8809133939	9.51981595495	2.52296227809
2	0.418603057683	-0.327301407575	0.350280662447	0.335951102021	-0.301468453426	0.510967663328	0.120192459957	-0.0574933848515	-0.00961073373067	0.0316188053499	-0.0490603765528	-0.0175674087093	-0.00630199661332	-0.0729985502441	0.00167787145695	0.108309121905	-0.00539884711715	0.0337407658968	0.11646053357	-0.0122986576622	0.139373278567	-42.2764010806	8.04470335969	40.1856165671
3	0.041648821883	0.0258892047694	0.0412683968005	0.110917588157	-0.138476235886	0.116399480716	0.0821970395957	0.0949800932652	-0.0674842179912	-0.237881946238	0.0544190442323	-0.258701444465	-0.173992939419	0.128082586045	0.0216045673081	0.17207201389	-0.0219390658983	0.0341259178595	0.243072864602	-0.0247964741241	0.253506675743	-2.49824770103	-7.87983981243	22.7215235364
4	0.214660647486	0.207809523208	-0.0950940002374	0.499983447338	0.145480563172	0.451063858545	-0.0615975560372	0.0209420953081	-0.033854295628	-0.0330976560688	0.0208364745084	-0.170186041329	-0.0592871797968	-0.019071961857	-0.0530104101155	0.113704648756	0.00261687832607	-0.0182539179794	0.135528427758	0.0110903185295	0.192752244735	-3.24326207799	-4.98173924819	31.5582464573
5	0.0134035679285	-0.0341265173949	-0.06205229708	0.116042125316	0.177548776438	0.299055585553	0.0805919514546	0.15819472294	0.274441048084	-0.1652840897	0.0412661001362	-0.0713500962465	-0.294801158138	0.0605618735389	0.541069199052	0.335598329005	-0.0988198406364	0.00284657712901	0.36621015637	0.590534892973	0.191794974162	8.5739819584	9.72435601171	-7.20574158799
6	0.855007128539	0.306998936475	0.160229178242	1.32220140877	-0.167461914611	1.50372226538	-0.301113675647	-0.202630336729	0.298396488296	0.564215911592	-0.23169014023	-0.629950255648	-0.510397161426	0.0684139549815	-0.772457355277	0.314188418701	-0.0340937464258	-0.145684481572	0.179145272759	0.145841732811	0.404857939082	4.91503044761	1.93571101968	2.24863018304
7	0.238640385242	-0.103483199196	0.0354805584056	0.666848922959	0.0212586018335	0.489854146034	-0.0134436612351	-0.021988409449	0.0117878935807	-0.0602496283518	0.0144296991683	-0.0285824809318	-0.0897580672539	-0.0278048324162	3.6046352726E-5	0.0591371579416	-0.0111992668645	-0.00681591103056	0.0747648950098	-0.00574588055477	0.122361363659	-0.545240789508	15.4208251439	34.8941938765
8	0.193813187838	-0.327652046857	0.162778195015	0.364794083517	-0.18185488076	0.171952169298	0.117938433352	-0.0550286192513	0.0253487405507	-0.0509930935531	-0.0332776953678	-0.0195147113224	0.026680304901	-0.108997608894	-7.28335812092E-5	0.301688836772	-0.0173430805689	0.000281305347756	0.273818619829	-0.0172976732131	0.200741994531	-4.29740353622	15.848200939	-2.76874834251
9	0.0229690308418	0.030040981742	0.0255695519091	0.0468842468777	-0.0165949314287	0.12491743974	0.23785919314	0.135875367727	0.0255361761246	0.00699679276573	-0.126325602332	0.00293236135597	-0.157227957751	-0.0116878102698	0.000640594285096	0.230569290887	0.0250553464719	-0.00591627878282	0.2423563487	0.0173311450729	0.198130020508	-35.9737737882	31.6469077122	15.1616604294
10	0.0222912959636	0.0377762310337	-0.0170365404981	0.045643781019	-0.0140963183808	0.0689358581419	-0.16001214516	0.00637940819232	0.00202070811341	0.18947434648	-0.0759643224036	-0.370350442513	-0.159210963662	0.41545652819	-0.00175080747649	0.329720727367	-0.0252208146576	0.0103057100922	0.408455063108	0.0957861191086	0.32112120417	-26.6513546075	32.8482170305	5.8706876354
11	0.346703041426	-0.104061426591	0.0806337142604	0.309351420482	0.0819983623799	0.3304497558	-0.289577453352	0.0165861558423	-0.00619210852624	-0.238032950779	0.193700404784	0.0895714093721	0.0260594196972	-0.100152667656	-0.062212752338	0.252150842176	-0.00791022580358	0.047429048613	0.157486300345	0.00694678377137	0.138694772111	-37.5062243607	30.1318376227	3.30685795871
12	0.307494421888	0.0106931983084	0.0619970123787	0.300292057664	0.114372965151	0.640566479032	0.0117978708296	-0.0476573894509	-0.00737011482626	-0.0963223312043	0.0858071296308	-0.0959886392447	-0.0655271155127	0.00344160319653	0.0161923606622	0.0901937206942	0.00600534765495	0.0333196233094	0.0937590286067	0.0188251500715	0.143992291432	-36.3032054995	24.1249074839	19.2109511317
13	0.306537151839	-0.193565490306	-0.11615199462	0.42098651213	0.00736905648769	0.462614355624	0.0208230970566	0.115964711838	0.0449460562261	0.0208856480141	0.0434586737745	-0.0811641023617	-0.0935883750943	0.141956583461	0.14652099932	0.150880668922	-0.0387044284823	0.00806301141681	0.189053378564	0.0074873894107	0.185405222821	-32.1463241431	22.384720234	36.0830398703
14	0.169849431889	0.196500658022	-0.0350558049939	0.227669866357	-0.0141164366491	0.0276271133426	0.0677260157929	0.0433116668356	0.0147004955438	-0.0895727255578	-0.0868576193296	0.154150817594	0.0838052909248	-0.0827796112866	-0.00427811559876	0.257862560154	0.0270004536211	0.0303909381342	0.124525365532	-0.0204434842067	0.171064031852	-38.8326798486	3.22209634365	5.27110952213

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 25 through 106A)
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 107 through 209 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 1 through 17 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 18 through 119 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 120 through 136 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 137 through 213 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 1 through 106A)
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 107 through 209 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1 through 17 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 18 through 32 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 33 through 82 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 82A through 145 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 146 through 213 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 1 through 24 )

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