PDB-7b4u: Broadly neutralizing DARPin bnD.2 in complex with the HIV-1 envel...

ID or keywords:

Entry

Database: PDB / ID: 7b4u

Title

Broadly neutralizing DARPin bnD.2 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)

Components

Broadly neutralizing DARPin bnD.2
HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)

Keywords

DE NOVO PROTEIN / HIV / V3 / conformation / neutralization / DARPins / antibodies

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.45 Å

Authors

Friedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. ...

Funding support

Switzerland, 3items

Organization	Grant number	Country
Swiss National Science Foundation	310030_192689	Switzerland
Swiss National Science Foundation	310030B_166676	Switzerland
Swiss National Science Foundation	31003A_146278	Switzerland

Citation

Journal: Nat Commun / Year: 2021
Title: Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization.
Authors: Friedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. / Morin, M. / Eroglu, M. / Liechti, T. / Ivan, B. / ...

History

Deposition	Dec 2, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 15, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	May 1, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7b4u.cif.gz	185.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7b4u.ent.gz	150.7 KB	Display	PDB format
PDBx/mmJSON format	7b4u.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/b4/7b4u ftp://data.pdbj.org/pub/pdb/validation_reports/b4/7b4u	HTTPS FTP

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Related structure data

Related structure data	7b4tC 7b4vC 7b4wC 7dneC 7dnfC 7dngC C: citing same article (ref.)
Similar structure data	1py2-1 3osj-4 6ef9-d 1bjj-6 6d34-1 5kjx-d 5yt7-1 5o3d-d 6uad-d 1ivt-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	#70 - Oct 2005 Designer Proteins similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Broadly neutralizing DARPin bnD.2

C: Broadly neutralizing DARPin bnD.2

D: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)

B: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)

hetero molecules

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

1

A: Broadly neutralizing DARPin bnD.2

B: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)

hetero molecules

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

2

C: Broadly neutralizing DARPin bnD.2

D: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.120, 69.290, 75.280
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Broadly neutralizing DARPin bnD.2 Mass: 13744.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide	HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505) Mass: 1603.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.36 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion Details: 0.2M Ca Acetate, 0.1M Na Cacodylate pH 6.5, 25% PEG 2K MME

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1.00004 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2015

Radiation

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

Radiation wavelength

Wavelength: 1.00004 Å / Relative weight: 1

Reflection

Resolution: 1.45→42.291 Å / Num. obs: 47687 / % possible obs: 98.9 % / Redundancy: 12.088 % / B_iso Wilson estimate: 15.68 Å² / CC_1/2: 1 / R_merge(I) obs: 0.045 / R_rim(I) all: 0.047 / Χ²: 0.95 / Net I/σ(I): 29.6 / Num. measured all: 576452 / Scaling rejects: 1087

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.45-1.49	10.437	0.426	5.5	35172	3526	3370	0.938	0.448	95.6
1.49-1.53	12.134	0.35	7.66	41303	3408	3404	0.967	0.366	99.9
1.53-1.57	12.277	0.305	8.75	40896	3335	3331	0.976	0.318	99.9
1.57-1.62	12.391	0.255	10.65	40060	3240	3233	0.985	0.267	99.8
1.62-1.67	12.35	0.216	12.59	38779	3143	3140	0.989	0.226	99.9
1.67-1.73	12.153	0.177	14.79	36775	3044	3026	0.991	0.185	99.4
1.73-1.8	11.617	0.139	17.49	33665	2935	2898	0.994	0.146	98.7
1.8-1.87	11.782	0.113	20.82	32602	2845	2767	0.996	0.119	97.3
1.87-1.96	12.328	0.088	26.51	33373	2715	2707	0.998	0.092	99.7
1.96-2.05	12.216	0.073	31.35	31993	2630	2619	0.998	0.076	99.6
2.05-2.16	12.098	0.06	36.52	29749	2471	2459	0.999	0.063	99.5
2.16-2.29	11.974	0.056	38.83	28054	2353	2343	0.999	0.059	99.6
2.29-2.45	11.742	0.048	43.91	25868	2227	2203	0.999	0.05	98.9
2.45-2.65	11.513	0.042	47.99	22946	2059	1993	0.999	0.044	96.8
2.65-2.9	13.127	0.037	58.13	25413	1936	1936	0.999	0.039	100
2.9-3.24	13.356	0.034	65.59	23252	1743	1741	0.999	0.035	99.9
3.24-3.74	13.124	0.029	74.83	20264	1557	1544	1	0.03	99.2
3.74-4.59	12.45	0.026	80.95	16372	1337	1315	1	0.027	98.4
4.59-6.48	12.157	0.025	79.92	12485	1053	1027	0.999	0.026	97.5
6.48-42.291	11.777	0.023	83.99	7431	637	631	1	0.024	99.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 1.45→42.291 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1729	2386	5.02 %
R_work	0.1457	45177	-
obs	0.1471	47563	98.83 %

Solvent computation

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

Displacement parameters

B_iso max: 110.14 Å² / B_iso mean: 24.4042 Å² / B_iso min: 9.5 Å²

Refinement step

Cycle: final / Resolution: 1.45→42.291 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2118	0	2	406	2526
B_iso mean	-	-	19.81	34.65	-
Num. residues	-	-	-	-	287

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2312
X-RAY DIFFRACTION	f_angle_d	0.952	3164
X-RAY DIFFRACTION	f_chiral_restr	0.068	367
X-RAY DIFFRACTION	f_plane_restr	0.007	427
X-RAY DIFFRACTION	f_dihedral_angle_d	19.381	838

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.4501-1.4797	0.2826	131	0.2474	2499	94
1.4797-1.5118	0.2407	144	0.202	2664	100
1.5118-1.547	0.1984	145	0.1905	2640	100
1.547-1.5857	0.2003	132	0.1729	2631	100
1.5857-1.6286	0.2083	130	0.176	2661	100
1.6286-1.6765	0.2227	169	0.1747	2631	100
1.6765-1.7306	0.2345	147	0.1659	2622	99
1.7306-1.7925	0.1943	144	0.1695	2634	99
1.7925-1.8642	0.1868	119	0.1676	2584	97
1.8642-1.9491	0.1667	145	0.1489	2659	100
1.9491-2.0518	0.1838	157	0.1489	2651	99
2.0518-2.1804	0.164	144	0.1375	2655	99
2.1804-2.3487	0.147	142	0.1261	2675	99
2.3487-2.585	0.16	137	0.128	2639	97
2.585-2.959	0.1669	118	0.1346	2739	100
2.959-3.7277	0.1674	119	0.1322	2765	100
3.7277-42.291	0.1512	163	0.1402	2828	98

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	1.8158	-0.6157	-2.6432	1.6974	0.6243	5.4607	-0.3298	-0.0017	0.9386	0.0052	-0.0676	-0.6158	-0.6019	0.6467	0.1628	0.187	-0.0299	-0.0853	0.2065	0.0536	0.2999	1.7616	23.8921	-17.4714
2	3.4793	-3.9387	0.3674	6.9574	-0.1002	0.0901	0.112	0.996	-0.146	-0.4849	-0.2602	-0.2795	0.5068	1.1356	0.0271	0.2375	0.1383	0.0257	0.4302	-0.0036	0.187	1.0952	16.9293	-24.6741
3	2.147	-0.4548	0.883	1.6957	0.3619	2.8779	0.0793	0.1181	0.1179	-0.0382	-0.0549	-0.147	0.0864	0.2472	-0.0328	0.1407	0.0103	0.0174	0.1168	0.0145	0.1607	-0.0137	18.9808	-12.363
4	1.8648	-0.45	0.7857	5.9393	-0.3117	6.0367	0.2053	0.3046	-0.3382	-0.606	-0.1725	-0.0386	0.5057	0.2687	-0.0561	0.2357	0.036	-0.0013	0.1152	-0.0083	0.1454	-4.186	10.1554	-19.1721
5	0.8041	-0.1272	0.2667	0.5511	-0.2308	0.9507	-0.0069	-0.0147	-0.0754	-0.0438	0.0078	-0.0353	0.065	0.0113	0.0084	0.1337	0.003	-0	0.1042	0.0019	0.1394	-6.3264	15.5873	-6.2021
6	3.2677	-3.8474	4.8499	4.7003	-5.6582	7.3184	0.2766	0.1129	-0.5196	-0.4784	-0.026	0.3609	0.4207	-0.081	-0.2154	0.167	-0.0055	-0.0126	0.1101	-0.0224	0.1836	-12.9356	7.402	-13.0704
7	1.9105	-0.8923	-1.2034	6.065	5.2243	6.6126	0.0296	-0.0802	-0.1252	0.2569	0.0239	-0.0468	0.2829	-0.0734	0.002	0.1415	-0.0045	-0.0056	0.1067	0.0294	0.1364	-9.0173	12.3571	1.3514
8	6.2279	-1.5336	2.1116	3.4514	-1.2346	4.9215	0.0407	-0.2809	0.0728	0.1725	-0.0986	0.0574	-0.0221	-0.2201	0.059	0.1218	-0.0147	0.0108	0.121	-0.0024	0.1431	-19.1394	15.834	-1.8462
9	4.6653	-2.8258	1.3717	6.5466	-2.6759	3.0148	-0.0541	-0.0481	-0.8565	0.015	0.1847	0.2778	0.5495	-0.3761	-0.2656	0.2102	-0.0514	0.0289	0.1488	0.0132	0.268	-20.219	6.0138	-3.4891
10	2.1078	-1.7695	2.0583	7.9374	-1.5727	2.1269	-0.1787	-0.6393	0.2343	0.8751	0.3179	0.0223	-0.3703	-0.5578	-0.1374	0.2351	0.0493	0.0216	0.248	0.0461	0.2188	-23.384	27.6466	-16.6006
11	3.4804	1.2885	4.9613	4.9771	2.1716	7.3112	-0.0802	-0.1042	-0.593	0.0687	0.3108	0.4306	0.5968	-0.5501	-0.255	0.1849	-0.0604	-0.0076	0.2286	0.0688	0.2319	-24.8387	18.6763	-19.3382
12	2.6077	0.2729	-0.2734	2.2253	-0.813	2.1566	0.0345	-0.0422	-0.0921	-0.0212	0.0684	0.1645	0.1057	-0.1976	-0.0871	0.1324	-0.01	-0.0185	0.1162	0.0138	0.1218	-18.2918	29.082	-27.298
13	6.4566	1.249	0.0677	0.867	2.0341	6.5174	0.1755	0.1075	-0.5617	-0.2722	0.0774	0.1247	0.7504	-0.0213	-0.2316	0.2687	-0.0238	-0.0414	0.1073	-0.0165	0.1631	-12.9938	21.0394	-35.562
14	5.1297	3.133	-0.6465	8.2231	-1.4682	3.7826	0.0274	-0.0053	0.1447	-0.3201	-0.0353	-0.0957	-0.0113	0.0933	0.01	0.1141	0.0215	-0.0047	0.1102	0.0085	0.0975	-12.0355	35.8306	-37.4792
15	6.0319	-0.9509	2.1325	4.3725	-2.0821	8.8638	0.0307	0.1754	0.2173	-0.1116	-0.037	-0.3468	-0.1987	0.3411	0.0242	0.1355	0.0102	0.0146	0.1476	0.0075	0.1771	-1.9323	31.9232	-34.5303
16	5.6947	-2.8682	0.1459	7.4092	-2.189	5.4926	0.3794	0.9979	-0.2556	-0.6161	-0.2118	-0.0523	1.0861	0.564	-0.199	0.2851	0.0566	0.0385	0.3128	-0.0345	0.1823	-4.8906	25.7295	-42.8643
17	7.1743	-4.2093	3.986	9.1864	-5.5364	3.8899	0.3699	-0.1986	-0.3839	0.1054	-0.1793	-0.3756	0.3633	0.1417	-0.1848	0.1812	-0.0189	-0.0455	0.1536	0.0253	0.2019	-2.1417	34.2706	-24.0315
18	6.566	-1.2737	1.893	2.6897	-4.1285	7.3616	0.2459	-0.4693	-0.1756	0.5309	-0.1888	-0.3062	-0.1547	0.0402	0.1178	0.1986	-0.0158	-0.0277	0.1494	0.01	0.151	-8.6471	35.5295	-20.7218
19	6.3503	-4.5868	5.5209	3.4829	-3.975	4.7943	0.2732	-0.1046	-0.4271	-0.1091	0.0122	0.1997	0.2265	-0.1762	-0.2764	0.1633	0.0076	0	0.1287	0.0061	0.1567	-16.4737	25.8219	-5.1534
20	3.2882	-0.8328	-1.6023	6.2213	-2.6161	4.2086	0.1666	0.1038	0.1727	-0.132	-0.0815	-0.0939	-0.1309	-0.1209	-0.0726	0.1302	0.015	-0.0062	0.0995	0.0102	0.1507	-8.9192	27.3745	-7.416

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 12 through 24 )	A	12 - 24
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 35 )	A	25 - 35
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 60 )	A	36 - 60
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 61 through 69 )	A	61 - 69
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 70 through 93 )	A	70 - 93
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 94 through 102 )	A	94 - 102
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 103 through 116 )	A	103 - 116
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 117 through 126 )	A	117 - 126
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 127 through 139 )	A	127 - 139
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 13 through 24 )	C	13 - 24
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 25 through 35 )	C	25 - 35
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 36 through 93 )	C	36 - 93
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 94 through 102 )	C	94 - 102
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 103 through 116 )	C	103 - 116
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 117 through 126 )	C	117 - 126
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 127 through 139 )	C	127 - 139
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 1 through 6 )	B	1 - 6
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 7 through 15 )	B	7 - 15
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 6 )	D	1 - 6
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 7 through 15 )	D	7 - 15

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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+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

-
Phasing

-
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