PDB-6apd: Crystal structure of RSV F bound by AM22 and the infant antibody ...

ID or keywords:

Entry

Database: PDB / ID: 6apd

Title

Crystal structure of RSV F bound by AM22 and the infant antibody ADI-19425

Components

AM22 Fab Heavy Chain,IGH@ protein
AM22 Fab Light Chain,Uncharacterized protein
Fusion glycoprotein F0,Envelope glycoprotein
IGL@ protein
Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain

Keywords

IMMUNE SYSTEM / viral glycoprotein /

immunoglobulin / infant /

complex

Function / homology

Function and homology information

positive regulation of syncytium formation by virus / positive regulation of B cell activation /

phagocytosis, recognition /

phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / host cell Golgi membrane /

immunoglobulin complex /

complement activation, classical pathway /

antigen binding ...
Similarity search - Function

Biological species

Respiratory syncytial virus

Human immunodeficiency virus 1

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 4.1 Å

Authors

Wrapp, D. / McLellan, J.S.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32GM008704	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41GM103393	United States

Citation

Journal: Immunity / Year: 2018
Title: Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation.
Authors: Goodwin, E. / Gilman, M.S.A. / Wrapp, D. / Chen, M. / Ngwuta, J.O. / Moin, S.M. / Bai, P. / Sivasubramanian, A. / Connor, R.I. / Wright, P.F. / Graham, B.S. / McLellan, J.S. / Walker, L.M.

History

Deposition	Aug 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6apd.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb6apd.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	6apd.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/ap/6apd ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apd	HTTPS FTP

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Related structure data

Related structure data	6apbC 6apcC C: citing same article (ref.)
Similar structure data	6n1v-d 22442 22847 6593 9320 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#170 - Feb 2014 Broadly Neutralizing Antibodies similarity (6) #21 - Sep 2001 Antibodies similarity (3) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #246 - Jun 2020 SARS-CoV-2 Spike similarity (2) #231 - Mar 2019 Measles Virus Proteins similarity (2)

Deposited unit

A: Fusion glycoprotein F0,Envelope glycoprotein

B: Fusion glycoprotein F0,Envelope glycoprotein

C: Fusion glycoprotein F0,Envelope glycoprotein

D: AM22 Fab Heavy Chain,IGH@ protein

E: AM22 Fab Light Chain,Uncharacterized protein

F: AM22 Fab Heavy Chain,IGH@ protein

G: AM22 Fab Light Chain,Uncharacterized protein

H: AM22 Fab Heavy Chain,IGH@ protein

I: AM22 Fab Light Chain,Uncharacterized protein

J: Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain

K: Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain

L: IGL@ protein

M: IGL@ protein

N: Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain

O: IGL@ protein

474 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	229.470, 229.470, 304.050
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain E and resid 1 through 211)
2	1	(chain G and resid 1 through 211)
3	1	chain I
1	2	chain J
2	2	chain K
3	2	chain N
1	3	chain L
2	3	chain M
3	3	chain O
1	4	chain D
2	4	(chain F and resid 1 through 215)
3	4	chain H
1	5	(chain A and (resid 27 through 97 or resid 137 through 515))
2	5	(chain B and (resid 27 through 97 or resid 137 through 515))
3	5	(chain C and resid 27 through 515)

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain E and resid 1 through 211)	E	1 - 211
2	1	1	(chain G and resid 1 through 211)	G	1 - 211
3	1	1	chain I	I	1 - 211
1	1	2	chain J	J	1 - 214
2	1	2	chain K	K	1 - 214
3	1	2	chain N	N	1 - 214
1	1	3	chain L	L	2 - 209
2	1	3	chain M	M	2 - 209
3	1	3	chain O	O	2 - 209
1	1	4	chain D	D	1 - 215
2	1	4	(chain F and resid 1 through 215)	F	1 - 215
3	1	4	chain H	H	1 - 215
1	1	5	(chain A and (resid 27 through 97 or resid 137 through 515))	A	27 - 97
1	2	5	(chain A and (resid 27 through 97 or resid 137 through 515))	A	137 - 515
2	1	5	(chain B and (resid 27 through 97 or resid 137 through 515))	B	27 - 97
2	2	5	(chain B and (resid 27 through 97 or resid 137 through 515))	B	137 - 515
3	1	5	(chain C and resid 27 through 515)	C	27 - 515

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	Fusion glycoprotein F0,Envelope glycoprotein Mass: 63775.891 Da / Num. of mol.: 3 Mutation: N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Respiratory syncytial virus, (gene. exp.) Human immunodeficiency virus 1 Production host: Homo sapiens (human) References: UniProt: C3UPB8, UniProt: M1E1E4, UniProt: P03420*PLUS
#2: Antibody	AM22 Fab Heavy Chain,IGH@ protein Mass: 24123.217 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Antibody	AM22 Fab Light Chain,Uncharacterized protein Mass: 23304.953 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#4: Antibody	Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE Mass: 23881.695 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-21 / Production host: Homo sapiens (human) / References: UniProt: A0A0B4J1V1, UniProt: P0DOX5
#5: Antibody	IGL@ protein / Mass: 22955.275 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX4

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.22 Å³/Da / Density % sol: 70.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 10% PEG 4000 10% 2-propanol 0.1 M sodium citrate pH 5.5

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Data collection

Diffraction

Mean temperature: 80 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97925 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.97925 Å / Relative weight: 1

Reflection

Resolution: 4.1→50.96 Å / Num. obs: 64175 / % possible obs: 99.9 % / Redundancy: 12.2 % / B_iso Wilson estimate: 117.98 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.364 / R_pim(I) all: 0.108 / R_rim(I) all: 0.38 / Net I/σ(I): 6.3 / Num. measured all: 785734 / Scaling rejects: 122

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
4.1-4.2	13	1.545	57821	4439	0.609	0.443	1.608	1.9	100
18.79-50.96	8.2	0.055	6056	743	0.997	0.021	0.06	24.9	94.7

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
Aimless	0.5.17	data scaling
PDB_EXTRACT	3.22	data extraction
iMOSFLM	7.2.1	data reduction
PHASER	2.57	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 4.1→50.958 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2562	3292	5.14 %
R_work	0.2037	60792	-
obs	0.2063	64084	99.96 %

Solvent computation

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

Displacement parameters

B_iso max: 502 Å² / B_iso mean: 166.2388 Å² / B_iso min: 66.22 Å²

Refinement step

Cycle: final / Resolution: 4.1→50.958 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30005	0	0	0	30005
Num. residues	-	-	-	-	3968

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	30657
X-RAY DIFFRACTION	f_angle_d	0.66	41703
X-RAY DIFFRACTION	f_chiral_restr	0.046	4854
X-RAY DIFFRACTION	f_plane_restr	0.005	5279
X-RAY DIFFRACTION	f_dihedral_angle_d	4.935	18334

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	E	2960	X-RAY DIFFRACTION	9.34	TORSIONAL
1	2	G	2960	X-RAY DIFFRACTION	9.34	TORSIONAL
1	3	I	2960	X-RAY DIFFRACTION	9.34	TORSIONAL
2	1	J	3076	X-RAY DIFFRACTION	9.34	TORSIONAL
2	2	K	3076	X-RAY DIFFRACTION	9.34	TORSIONAL
2	3	N	3076	X-RAY DIFFRACTION	9.34	TORSIONAL
3	1	L	2935	X-RAY DIFFRACTION	9.34	TORSIONAL
3	2	M	2935	X-RAY DIFFRACTION	9.34	TORSIONAL
3	3	O	2935	X-RAY DIFFRACTION	9.34	TORSIONAL
4	1	D	3012	X-RAY DIFFRACTION	9.34	TORSIONAL
4	2	F	3012	X-RAY DIFFRACTION	9.34	TORSIONAL
4	3	H	3012	X-RAY DIFFRACTION	9.34	TORSIONAL
5	1	A	6315	X-RAY DIFFRACTION	9.34	TORSIONAL
5	2	B	6315	X-RAY DIFFRACTION	9.34	TORSIONAL
5	3	C	6315	X-RAY DIFFRACTION	9.34	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
4.1-4.1585	0.2984	121	0.2881	2497	2618	100
4.1585-4.2206	0.3438	134	0.2891	2470	2604	100
4.2206-4.2865	0.3279	148	0.2717	2500	2648	100
4.2865-4.3567	0.3175	150	0.2586	2476	2626	100
4.3567-4.4318	0.2661	157	0.244	2477	2634	100
4.4318-4.5124	0.2601	146	0.2278	2494	2640	100
4.5124-4.5991	0.2921	131	0.2308	2505	2636	100
4.5991-4.6929	0.2829	143	0.2158	2492	2635	100
4.6929-4.7949	0.2362	113	0.2071	2529	2642	100
4.7949-4.9063	0.2651	134	0.205	2510	2644	100
4.9063-5.0289	0.2717	111	0.2073	2523	2634	100
5.0289-5.1648	0.2397	115	0.2045	2532	2647	100
5.1648-5.3166	0.2632	143	0.2062	2528	2671	100
5.3166-5.488	0.2673	134	0.2116	2511	2645	100
5.488-5.6839	0.2645	125	0.2118	2537	2662	100
5.6839-5.9112	0.2642	140	0.2168	2529	2669	100
5.9112-6.1798	0.2837	138	0.2061	2532	2670	100
6.1798-6.505	0.2765	142	0.2042	2534	2676	100
6.505-6.9116	0.2674	146	0.1916	2553	2699	100
6.9116-7.4437	0.2459	145	0.1867	2537	2682	100
7.4437-8.1901	0.2406	132	0.1616	2583	2715	100
8.1901-9.3688	0.2064	134	0.1528	2589	2723	100
9.3688-11.7796	0.1713	139	0.1399	2621	2760	100
11.7796-50.9616	0.2625	171	0.2165	2733	2904	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	0.7288	0.3011	0.2322	0.9669	-0.7524	2.1662	-0.0999	-0.1008	0.3516	-0.0436	0.077	-0.0011	-0.0983	0.2844	0.041	0.8276	0.0157	-0.1531	1.0005	-0.1322	1.1397	10.1482	66.0543	-36.9534
2	2.2563	1.3849	-0.0094	1.5211	0.0837	0.3115	0.0301	-0.0704	0.1707	-0.0544	-0.0585	0.0132	0.0317	0.1029	0.0275	0.9042	0.0848	-0.1138	1.0501	0.0409	1.093	20.4914	48.9789	-36.9968
3	1.5795	0.3676	-0.5674	0.4657	-0.0102	1.2415	-0.2017	-0.0091	0.4656	-0.1601	0.1594	0.0997	-0.0945	0.0548	0.0467	0.6744	0.0101	-0.1549	0.9443	-0.0256	0.8003	6.9811	52.2917	-51.1553
4	3.37	1.8769	0.7179	2.4842	0.9544	2.2952	0.1955	-0.6728	-1.0009	0.9077	0.1307	-1.1413	0.8708	-0.2314	-0.3042	1.3742	0.3068	-0.3077	1.5954	0.1663	1.2737	-4.0293	10.5731	21.6663
5	2.1072	2.0255	-1.1815	6.1082	-2.193	2.3218	0.2068	-0.5651	-0.6075	0.8148	0.3793	0.4786	0.4754	-0.6001	-0.5578	1.306	0.1279	-0.2728	1.9698	0.3126	1.4352	-20.9878	5.7342	17.1619
6	2.2778	-0.7921	-0.8489	3.1856	-0.954	6.5004	-0.9299	-1.2973	1.2976	1.1808	0.573	-0.4045	-1.153	-0.606	0.371	1.2824	0.5047	-0.3576	1.9835	-0.5468	1.6853	-50.3838	65.9096	7.0739
7	2.9594	-3.4009	-1.4602	5.0192	0.6826	4.4885	-1.5162	-2.1299	-0.5025	1.9621	0.947	0.7754	-0.1116	-0.4548	0.5801	1.5832	0.5423	-0.0058	2.5957	0.0354	1.6631	-49.5997	50.2094	15.9776
8	9.2723	2.2906	0.3701	2.5318	0.0143	2.5353	0.2119	0.3084	-1.3932	-0.4588	-0.329	-0.2886	0.3807	-0.1008	0.0756	1.1844	0.0613	-0.1553	0.8082	-0.047	1.322	-49.9362	5.4595	-35.1307
9	5.3042	-0.5499	1.5585	2.7539	1.0311	3.7912	0.8255	-1.1086	-0.8212	0.4628	-0.771	1.2964	0.9911	-0.7967	-0.0214	1.2876	-0.2607	0.0041	1.3084	0.171	1.3205	-56.789	12.2511	-19.8171
10	5.3768	-1.5796	5.6156	1.0493	-0.3754	6.8889	0.1277	0.2323	0.0167	-0.1238	0.0344	-0.1836	-0.1275	0.464	-0.1877	1.001	-0.1554	-0.0955	0.7646	0.0337	1.0575	-22.9308	45.4411	-94.3358
11	2.6379	-1.6126	0.696	4.9949	-0.8673	3.4537	-0.1746	0.0187	-0.3106	0.2201	0.0748	-0.8994	0.8742	0.733	0.1001	1.0887	0.4167	-0.2291	1.3773	-0.019	1.3054	56.5033	13.9432	-20.0747
12	6.9513	-0.0981	3.9423	0.1322	0.5893	5.2902	-0.5656	-0.1522	0.0388	-0.2805	0.1012	-0.2535	-0.6637	-0.1312	0.4898	0.86	-0.0454	0.0184	0.6386	0.0011	1.1046	-33.1112	57.4432	-87.0093
13	6.3971	-0.6691	1.2236	4.7693	-1.7955	3.7617	0.2041	-0.4811	-1.3399	-0.002	-0.2615	-0.9126	1.6862	0.2324	0.3033	1.7737	0.1844	0.0499	1.2421	-0.1211	1.3637	47.3061	1.9543	-29.0375
14	1.0672	0.6421	1.3772	7.9376	4.3422	5.5505	-0.2067	-0.5478	0.7238	-0.6666	0.034	0.3104	-0.9415	-0.4421	0.3085	1.0849	0.3439	-0.3109	1.426	-0.325	1.8308	7.0815	112.4554	-11.768
15	0.6853	1.1138	-0.0635	2.6335	1.8693	3.8724	0.1648	-0.5791	0.8702	0.292	0.0079	-0.1511	-0.2576	-0.5659	-0.2047	1.0395	0.3424	-0.2606	1.4424	-0.3102	1.9612	14.949	104.0355	1.2812

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 27 through 515)	A	27 - 515
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 27 through 517)	B	27 - 517
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 27 through 517)	C	27 - 517
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 1 through 215)	D	1 - 215
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 1 through 212)	E	1 - 212
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 1 through 216)	F	1 - 216
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 1 through 214)	G	1 - 214
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 1 through 215)	H	1 - 215
9	X-RAY DIFFRACTION	9	(chain 'I' and resid 1 through 211)	I	1 - 211
10	X-RAY DIFFRACTION	10	(chain 'J' and resid 1 through 214)	J	1 - 214
11	X-RAY DIFFRACTION	11	(chain 'K' and resid 1 through 214)	K	1 - 214
12	X-RAY DIFFRACTION	12	(chain 'L' and resid 2 through 209)	L	2 - 209
13	X-RAY DIFFRACTION	13	(chain 'M' and resid 2 through 209)	M	2 - 209
14	X-RAY DIFFRACTION	14	(chain 'N' and resid 1 through 214)	N	1 - 214
15	X-RAY DIFFRACTION	15	(chain 'O' and resid 2 through 209)	O	2 - 209

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