PDB-4n9g: Crystal Structure of a Computationally Designed RSV-Presenting Ep...

ID or keywords:

Entry

Database: PDB / ID: 4n9g

Title

Crystal Structure of a Computationally Designed RSV-Presenting Epitope Scaffold And Its Elicited Antibody 17HD9

Components

Antibody 17HD9, Heavy Chain
Antibody 17HD9, Light Chain
Epitope Scaffold rsv_1isea_FFL_001_C

Keywords

IMMUNE SYSTEM / Antibody / Hairpin / Epitope Scaffold

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Macaca mulatta (Rhesus monkey)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Carrico, C.T.D. / Strong, R.K.

Citation

Journal: Nature / Year: 2014
Title: Proof of principle for epitope-focused vaccine design.
Authors: Correia, B.E. / Bates, J.T. / Loomis, R.J. / Baneyx, G. / Carrico, C. / Jardine, J.G. / Rupert, P. / Correnti, C. / Kalyuzhniy, O. / Vittal, V. / Connell, M.J. / Stevens, E. / Schroeter, A. ...

History

Deposition	Oct 21, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4n9g.cif.gz	698.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4n9g.ent.gz	580.2 KB	Display	PDB format
PDBx/mmJSON format	4n9g.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/n9/4n9g ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n9g	HTTPS FTP

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Related structure data

Related structure data	4jlrC 4l8iC 3eo9S 3q6gS 3qhzS 3sobS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5e8d-d 3sf4-2 3sf4-1 6ywc-2 6z7z-2 6z7y-2 3qwo-2 4lmq-1 5u3j-d 6vtw-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) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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)

Deposited unit

A: Antibody 17HD9, Heavy Chain

B: Antibody 17HD9, Light Chain

C: Epitope Scaffold rsv_1isea_FFL_001_C

D: Epitope Scaffold rsv_1isea_FFL_001_C

E: Antibody 17HD9, Heavy Chain

F: Antibody 17HD9, Light Chain

H: Antibody 17HD9, Heavy Chain

L: Antibody 17HD9, Light Chain

M: Antibody 17HD9, Heavy Chain

N: Antibody 17HD9, Light Chain

Y: Epitope Scaffold rsv_1isea_FFL_001_C

Z: Epitope Scaffold rsv_1isea_FFL_001_C

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

1

A: Antibody 17HD9, Heavy Chain

B: Antibody 17HD9, Light Chain

C: Epitope Scaffold rsv_1isea_FFL_001_C

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

2

D: Epitope Scaffold rsv_1isea_FFL_001_C

E: Antibody 17HD9, Heavy Chain

F: Antibody 17HD9, Light Chain

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

3

H: Antibody 17HD9, Heavy Chain

L: Antibody 17HD9, Light Chain

Y: Epitope Scaffold rsv_1isea_FFL_001_C

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

4

M: Antibody 17HD9, Heavy Chain

N: Antibody 17HD9, Light Chain

Z: Epitope Scaffold rsv_1isea_FFL_001_C

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

Unit cell

Length a, b, c (Å)	64.213, 89.266, 104.304
Angle α, β, γ (deg.)	89.99, 102.73, 89.91
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	H
2	1	M
1	2	L
2	2	N
1	3	A
2	3	E
1	4	B
2	4	F
1	5	C
2	5	D
1	6	Y
2	6	Z

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	H	1 - 999
2	1	1	4	M	1 - 999
1	1	2	4	L	1 - 999
2	1	2	4	N	1 - 999
1	1	3	4	A	1 - 999
2	1	3	4	E	1 - 999
1	1	4	4	B	1 - 999
2	1	4	4	F	1 - 999
1	1	5	4	C	1 - 999
2	1	5	4	D	1 - 999
1	1	6	4	Y	1 - 999
2	1	6	4	Z	1 - 999

NCS ensembles :

ID
1
2
3
4
5
6

#1: Antibody	Antibody 17HD9, Heavy Chain Mass: 24461.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pHLsec / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody	Antibody 17HD9, Light Chain Mass: 23512.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pHLsec / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Protein	Epitope Scaffold rsv_1isea_FFL_001_C Mass: 14450.532 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Gene: Computationally designed variant of Ribosomal Recycling Factor Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 14% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2013
Radiation	Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→48.75 Å / Num. all: 78170 / Num. obs: 76354 / % possible obs: 97.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3.9 % / R_merge(I) obs: 0.076 / Net I/σ(I): 9.4
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 3.89 % / R_merge(I) obs: 0.212 / Mean I/σ(I) obs: 4.4 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
d*TREK		data reduction
d*TREK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS ...
Resolution: 2.5→48.75 Å / Cor.coef. F_o:F_c: 0.864 / Cor.coef. F_o:F_c free: 0.829 / SU B: 23.784 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29516	3829	5 %	RANDOM
R_work	0.26335	-	-	-
all	0.26496	76354	-	-
obs	0.26496	72525	97.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 41.108 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	-0.04 Å²	-0.02 Å²
2-	-	-0.02 Å²	-0.05 Å²
3-	-	-	-0.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→48.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14202	0	0	59	14261

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	14537
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9526
X-RAY DIFFRACTION	r_angle_refined_deg	0.961	1.955	19805
X-RAY DIFFRACTION	r_angle_other_deg	0.74	3	23409
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.836	5	1885
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.873	24.908	546
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.612	15	2280
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.563	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	2277
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	16209
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2762
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.332	2	9426
X-RAY DIFFRACTION	r_mcbond_other	0.048	2	3801
X-RAY DIFFRACTION	r_mcangle_it	0.622	3	15241
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.754	4	5111
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.192	6	4557
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	H	2703	MEDIUM POSITIONAL	0.26	0.5
1	H	2703	MEDIUM THERMAL	0.12	2
2	L	2704	MEDIUM POSITIONAL	0.24	0.5
2	L	2704	MEDIUM THERMAL	0.14	2
3	A	2666	MEDIUM POSITIONAL	0.28	0.5
3	A	2666	MEDIUM THERMAL	0.12	2
4	B	2687	MEDIUM POSITIONAL	0.27	0.5
4	B	2687	MEDIUM THERMAL	0.13	2
5	C	414	MEDIUM POSITIONAL	0.4	0.5
5	C	414	MEDIUM THERMAL	0.14	2
6	Y	435	MEDIUM POSITIONAL	0.38	0.5
6	Y	435	MEDIUM THERMAL	0.19	2

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.4	264	-
R_work	0.315	5430	-
obs	-	5430	97.53 %

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	2.821	0.5904	1.9586	2.6883	-0.7126	3.2693	-0.2809	-0.0625	0.1182	-0.0613	-0.1092	0.2525	-0.43	-0.0921	0.3901	0.1862	-0.0138	-0.0432	0.044	-0.0234	0.1649	26.1007	-62.015	34.3363
2	2.9169	1.9737	0.7861	4.5347	0.1794	1.4705	-0.0934	0.0783	0.0041	-0.0914	0.1125	0.1322	-0.0499	0.0264	-0.0191	0.0395	0.0137	-0.0212	0.1515	0.0046	0.0897	8.3516	-80.9445	9.6627
3	2.2415	0.7957	0.7276	2.5896	-1.2276	2.3502	0.0073	0.1192	0.0811	-0.0559	0.0003	0.0175	0.0879	0.2476	-0.0076	0.0609	0.0416	0.0173	0.1089	0.0107	0.0898	32.8675	-82.0083	37.2271
4	1.3072	0.068	-0.2978	2.1504	-0.719	4.6897	0.0154	0.042	-0.0696	-0.0081	-0.0393	-0.0692	0.2633	0.0206	0.0239	0.0367	-0.0185	-0.0387	0.0909	-0.0228	0.1187	20.4335	-89.5315	3.9013
5	2.6396	1.6221	-2.7136	1.1196	-0.1047	21.1059	0.0533	-0.0649	-0.2105	0.0354	-0.0333	-0.0896	-0.8763	0.7706	-0.0201	0.2833	-0.2086	-0.0386	0.1714	0.0513	0.1407	41.9365	-59.4871	54.7514
6	4.7553	-2.3281	-0.3585	1.4183	-3.1946	23.4453	-0.1151	-0.0608	0.068	0.1333	0.0237	-0.0406	-1.1958	-0.6551	0.0914	0.3745	0.2495	-0.0655	0.147	-0.0565	0.0736	7.3754	-14.3931	-59.1563
7	1.9814	-0.5132	1.5671	2.1556	1.0559	3.6825	-0.2481	-0.0049	0.0844	0.0175	-0.0765	-0.2143	-0.5129	0.0186	0.3246	0.2156	0.046	-0.0515	0.0591	0.0173	0.1646	22.5266	-17.3352	-39.6386
8	1.924	-0.8339	0.9357	3.324	-0.4928	2.0773	-0.0895	-0.0861	0.057	-0.0458	0.0792	-0.131	-0.0501	0.0343	0.0104	0.0587	0.0165	-0.006	0.098	-0.008	0.0992	39.8667	-35.3809	-15.8808
9	2.3696	-1.0534	1.1102	2.8352	0.9988	2.1152	0.0528	-0.1022	0.0268	-0.0082	-0.1112	0.0936	0.0845	-0.229	0.0583	0.0605	-0.0003	0.013	0.1148	-0.0125	0.1051	16.0001	-37.5246	-42.4181
10	1.1771	-0.6431	-0.5888	2.1914	0.2991	3.6087	-0.0352	-0.0341	-0.1026	0.1159	-0.0434	0.1319	0.2218	-0.1036	0.0787	0.032	0.0142	-0.0189	0.1132	0.0105	0.1191	28.3003	-44.9001	-9.1534
11	0.7628	-0.1211	-0.9946	1.7514	-1.2293	4.6176	0.0647	0.038	-0.029	-0.1058	-0.0107	0.0753	0.3359	-0.1637	-0.054	0.1123	0.0327	-0.0131	0.073	0.0095	0.1104	53.8833	-95.5081	-34.1935
12	1.6522	-0.3266	0.0082	3.7468	0.3948	2.5288	0.0548	-0.1459	0.1318	-0.0735	-0.0837	0.2587	-0.0497	-0.1612	0.0289	0.0052	0.0075	0.0176	0.1273	0.0037	0.1528	39.858	-79.4286	-7.2331
13	0.2222	-0.1798	-0.4153	0.3547	0.4208	2.555	0.0425	-0.0342	0.0178	-0.0585	-0.0431	-0.1105	-0.1391	0.1262	0.0006	0.0626	0.0068	0.0205	0.079	0.0194	0.1682	58.8681	-74.3924	-26.1642
14	0.7174	-0.5332	1.0395	1.559	-0.5507	4.6687	-0.0619	0.0023	0.0434	0.0923	0.008	-0.0475	-0.115	0.1826	0.0539	0.0777	-0.0014	0.0093	0.0906	-0.0091	0.1428	53.2825	-70.9423	1.3117
15	1.0578	0.2897	-0.8699	1.9023	1.9018	5.0402	0.0732	-0.0187	-0.0333	0.1723	0.0167	-0.1069	0.2752	0.2156	-0.0899	0.1056	-0.0212	-0.0184	0.0791	-0.0046	0.1302	59.011	-51.0361	28.9308
16	1.8522	0.4558	-0.498	3.4351	-1.0033	2.8575	0.0441	0.1099	0.1152	-0.0209	-0.0555	-0.224	-0.0317	0.1488	0.0114	0.0159	0.025	0.023	0.1228	0.0065	0.1306	73.147	-34.725	2.1241
17	1.2688	0.5009	-0.7813	2.7866	-0.4616	1.7514	0.0418	0.0454	0.0488	0.0453	-0.0307	0.1637	-0.1187	-0.1042	-0.0112	0.0664	0.0149	0.0317	0.117	-0.0017	0.1372	51.1433	-31.1654	30.541
18	1.3274	0.2046	0.8146	1.6681	0.6069	4.4335	-0.0538	0.0298	0.0447	-0.0585	0.0003	0.1166	-0.1415	-0.116	0.0535	0.0495	-0.0039	0.0199	0.067	0.024	0.1306	60.6625	-26.1907	-4.8155
19	0.2787	0.8576	1.3063	3.0376	1.1558	15.5338	0.0089	-0.0403	0.0685	-0.3092	-0.1016	-0.0098	0.3896	0.4511	0.0927	0.265	0.2328	0.0251	0.2114	-0.0398	0.1609	65.7073	-95.752	-56.1328
20	3.4868	1.1553	0.9456	6.3622	0.5678	7.8596	0.3136	0.0191	0.1328	0.4327	-0.4986	0.0625	0.4735	-0.3829	0.185	0.2427	-0.2009	0.0323	0.193	-0.0088	0.0853	47.4832	-51.613	48.392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 109
2	X-RAY DIFFRACTION	2	A	110 - 216
3	X-RAY DIFFRACTION	3	B	1 - 106
4	X-RAY DIFFRACTION	4	B	107 - 214
5	X-RAY DIFFRACTION	5	C	63 - 97
6	X-RAY DIFFRACTION	6	D	62 - 95
7	X-RAY DIFFRACTION	7	E	1 - 104
8	X-RAY DIFFRACTION	8	E	105 - 213
9	X-RAY DIFFRACTION	9	F	2 - 106
10	X-RAY DIFFRACTION	10	F	107 - 213
11	X-RAY DIFFRACTION	11	H	1 - 113
12	X-RAY DIFFRACTION	12	H	114 - 214
13	X-RAY DIFFRACTION	13	L	1 - 149
14	X-RAY DIFFRACTION	14	L	150 - 214
15	X-RAY DIFFRACTION	15	M	2 - 125
16	X-RAY DIFFRACTION	16	M	126 - 225
17	X-RAY DIFFRACTION	17	N	1 - 107
18	X-RAY DIFFRACTION	18	N	108 - 213
19	X-RAY DIFFRACTION	19	Y	63 - 95
20	X-RAY DIFFRACTION	20	Z	62 - 87

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About Yorodumi

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Yorodumi