PDB-6x7w: Vaccine-elicited mouse FP-targeting neutralizing antibody vFP49.0...

ID or keywords:

Entry

Database: PDB / ID: 6x7w

Title

Vaccine-elicited mouse FP-targeting neutralizing antibody vFP49.02 in complex with HIV fusion peptide (residue 512-519)

Components

HIV fusion peptide 512-519
antibody vFP49.02 heavy chain
antibody vFP49.02 light chain

Keywords

IMMUNE SYSTEM/VIRAL PROTEIN / HIV / fusion peptide / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Xu, K. / Kwong, P.D.

Citation

Journal: To Be Published
Title: Distinct Classes of HIV-1 Cross-Clade Neutralizing Antibodies Targeting Fusion Peptide Elicited in Mice by Diverse Immunization Regimens
Authors: Xu, K. / Kwong, P.D.

History

Deposition	May 30, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 2, 2021	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
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/6x7w ftp://data.pdbj.org/pub/pdb/validation_reports/x7/6x7w	HTTPS FTP

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Related structure data

Related structure data	6x78C 6cdoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6h0e-1 3o6l-d 4dgv-d 6mqr-d 4xh2-4 1kel-d 6xuk-d 1lo0-1 6bqb-d 3hr5-3 4m7j-d 1keg-d 5u4r-2 4osu-d 1tzg-2 4qth-1 5vkk-1 4jg1-d 1opg-d 2f19-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

6x78C

6cdoS

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) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: antibody vFP49.02 heavy chain

G: HIV fusion peptide 512-519

H: antibody vFP49.02 heavy chain

L: antibody vFP49.02 light chain

C: antibody vFP49.02 light chain

D: HIV fusion peptide 512-519

hetero molecules

99 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: antibody vFP49.02 heavy chain

C: antibody vFP49.02 light chain

D: HIV fusion peptide 512-519

hetero molecules

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

2

G: HIV fusion peptide 512-519

H: antibody vFP49.02 heavy chain

L: antibody vFP49.02 light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.881, 99.229, 137.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	L-442- HOH
2	1	L-496- HOH
3	1	C-443- HOH
4	1	C-491- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 1 through 129 or resid 133 through 214))
2	1	chain H
1	2	(chain C and (resid 1 through 99 or (resid 100...
2	2	(chain L and (resid 1 through 99 or (resid 100...
1	3	chain D
2	3	(chain G and resid 512 through 519)

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	GLU	GLU	ALA	ALA	(chain A and (resid 1 through 129 or resid 133 through 214))	A	A	1 - 129	1 - 139
1	2	1	ASN	ASN	ASP	ASP	(chain A and (resid 1 through 129 or resid 133 through 214))	A	A	133 - 214	143 - 224
2	1	1	GLU	GLU	ASP	ASP	chain H	H	C	1 - 214	1 - 224
1	1	2	ASP	ASP	GLY	GLY	(chain C and (resid 1 through 99 or (resid 100...	C	E	1 - 99	1 - 99
1	2	2	ALA	ALA	GLY	GLY	(chain C and (resid 1 through 99 or (resid 100...	C	E	100 - 101	100 - 101
2	1	2	ASP	ASP	GLY	GLY	(chain L and (resid 1 through 99 or (resid 100...	L	D	1 - 99	1 - 99
2	2	2	ALA	ALA	GLY	GLY	(chain L and (resid 1 through 99 or (resid 100...	L	D	100 - 101	100 - 101
2	3	2	ASP	ASP	GLU	GLU	(chain L and (resid 1 through 99 or (resid 100...	L	D	1 - 213	1 - 213
2	4	2	ASP	ASP	GLU	GLU	(chain L and (resid 1 through 99 or (resid 100...	L	D	1 - 213	1 - 213
2	5	2	ASP	ASP	GLU	GLU	(chain L and (resid 1 through 99 or (resid 100...	L	D	1 - 213	1 - 213
1	1	3	ALA	ALA	PHE	PHE	chain D	D	F	512 - 519	2 - 9
2	1	3	ALA	ALA	PHE	PHE	(chain G and resid 512 through 519)	G	B	512 - 519	2 - 9

NCS ensembles :

ID
1
2
3

#1: Antibody	antibody vFP49.02 heavy chain Mass: 25020.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Protein/peptide	HIV fusion peptide 512-519 Mass: 758.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Antibody	antibody vFP49.02 light chain Mass: 23620.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.42 Å³/Da / Density % sol: 49.18 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M ammonium sulfate , 0.1 M HEPES, pH 7.5, 20% w/v PEG8000, 10% w/v isopropanol

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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: Nov 15, 2019

Radiation

Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 102556 / % possible obs: 97.6 % / Redundancy: 6.1 % / R_merge(I) obs: 0.106 / R_pim(I) all: 0.051 / R_rim(I) all: 0.118 / Χ²: 1.755 / Net I/σ(I): 5.8 / Num. measured all: 622325

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.73	6.6	0.977	5178	0.797	0.412	1.063	0.667	99.8
1.73-1.76	6.6	0.813	5140	0.874	0.34	0.884	0.728	99.7
1.76-1.79	6.6	0.692	5190	0.882	0.294	0.754	0.793	99.5
1.79-1.83	6.5	0.593	5173	0.899	0.255	0.647	0.868	99.4
1.83-1.87	6.4	0.499	5101	0.934	0.216	0.546	1.003	99
1.87-1.91	6.2	0.434	5106	0.939	0.193	0.476	1.091	98.3
1.91-1.96	6	0.37	5092	0.952	0.169	0.408	1.242	97.9
1.96-2.02	5.4	0.306	5026	0.965	0.146	0.341	1.376	96.1
2.02-2.07	6.3	0.271	5078	0.978	0.12	0.298	1.453	97.9
2.07-2.14	6.4	0.231	5129	0.983	0.103	0.254	1.552	98.2
2.14-2.22	6.4	0.2	5098	0.985	0.09	0.221	1.677	97.6
2.22-2.31	6.2	0.174	5103	0.987	0.081	0.193	1.745	97.4
2.31-2.41	6.1	0.154	5095	0.991	0.072	0.17	1.766	97
2.41-2.54	5.9	0.134	5053	0.991	0.065	0.15	1.889	96.8
2.54-2.7	5.7	0.115	5059	0.992	0.058	0.13	1.98	96.1
2.7-2.91	5.2	0.096	5009	0.993	0.051	0.11	2.228	94.7
2.91-3.2	6.2	0.083	5113	0.994	0.041	0.093	2.664	96.7
3.2-3.66	6	0.069	5194	0.995	0.034	0.078	3.309	97.3
3.66-4.61	5.5	0.061	5175	0.995	0.032	0.07	3.976	96.6
4.61-50	5.4	0.059	5444	0.996	0.029	0.066	4.089	97.1

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.18_3845	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 6CDO

6cdo

Resolution: 1.7→34.94 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2483	5139	5.03 %
R_work	0.2144	96979	-
obs	0.2161	102118	96.43 %

Solvent computation

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

Displacement parameters

B_iso max: 98.9 Å² / B_iso mean: 27.5416 Å² / B_iso min: 12.3 Å²

Refinement step

Cycle: final / Resolution: 1.7→34.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6724	0	10	816	7550
B_iso mean	-	-	37.12	36.56	-
Num. residues	-	-	-	-	886

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1328	X-RAY DIFFRACTION	0.299	TORSIONAL
1	2	H	1328	X-RAY DIFFRACTION	0.299	TORSIONAL
2	1	C	1285	X-RAY DIFFRACTION	0.299	TORSIONAL
2	2	L	1285	X-RAY DIFFRACTION	0.299	TORSIONAL
3	1	D	42	X-RAY DIFFRACTION	0.299	TORSIONAL
3	2	G	42	X-RAY DIFFRACTION	0.299	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.72	0.3181	113	0.3037	2409	2522	73
1.72-1.74	0.3323	174	0.2983	3310	3484	100
1.74-1.76	0.278	158	0.2821	3296	3454	99
1.76-1.78	0.3127	195	0.2754	3313	3508	99
1.78-1.81	0.2761	162	0.2716	3274	3436	99
1.81-1.83	0.2982	185	0.2582	3279	3464	99
1.83-1.86	0.2448	183	0.2471	3268	3451	99
1.86-1.89	0.306	191	0.2414	3280	3471	99
1.89-1.92	0.2861	150	0.2339	3265	3415	98
1.92-1.95	0.2561	165	0.2248	3267	3432	98
1.95-1.98	0.2499	181	0.2242	3208	3389	97
1.98-2.02	0.2583	168	0.2201	3170	3338	96
2.02-2.05	0.231	168	0.218	3253	3421	97
2.05-2.1	0.2493	198	0.2118	3233	3431	98
2.1-2.14	0.2337	172	0.2069	3251	3423	98
2.14-2.19	0.239	160	0.2062	3285	3445	97
2.19-2.25	0.2774	165	0.2066	3269	3434	98
2.25-2.31	0.2292	158	0.2133	3247	3405	97
2.31-2.38	0.2807	182	0.2161	3201	3383	96
2.38-2.45	0.262	177	0.2166	3235	3412	97
2.45-2.54	0.293	184	0.2147	3225	3409	96
2.54-2.64	0.249	174	0.2129	3221	3395	96
2.64-2.76	0.2663	166	0.2165	3229	3395	95
2.76-2.91	0.2756	160	0.2165	3166	3326	94
2.91-3.09	0.268	175	0.2084	3237	3412	96
3.09-3.33	0.2442	174	0.2039	3290	3464	97
3.33-3.66	0.2617	192	0.1955	3276	3468	97
3.66-4.19	0.1951	177	0.1909	3331	3508	97
4.19-5.28	0.2062	152	0.1896	3323	3475	96
5.28-34.94	0.2336	180	0.2229	3368	3548	93

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	1.5246	-0.8614	-0.3845	0.9388	0.4386	1.8374	-0.0329	0.0523	-0.0087	0.0445	0.0167	-0.018	-0.079	-0.0642	-0.0037	0.1026	-0.006	0.0101	0.092	0.0046	0.1257	-10.5518	-22.0002	-65.613
2	0.5814	-0.2252	-0.4229	0.2309	0.4359	0.5795	0.0188	-0.0298	-0.0036	-0.0051	-0.0903	0.1	-0.1552	-0.228	-0.0152	0.2304	0.0147	-0.0003	0.1604	-0.0009	0.1596	-14.3425	-14.6226	-41.5073
3	0.9112	-0.1488	-0.6745	2.8563	-0.0925	1.4724	0.034	-0.0154	-0.0881	0.0069	0.0182	-0.0597	-0.0147	0.0975	0	0.2009	0.0292	-0.0188	0.1892	-0.0162	0.1783	-11.7289	-11.1223	-31.0111
4	0.0547	-0.0208	-0.0341	0.0349	-0.0508	0.1539	-0.047	-0.3368	0.0417	0.1096	0.1486	0.0875	-0.3107	0.2186	0.0039	0.2866	-0.025	-0.0598	0.2941	-0.07	0.2756	-4.3546	34.6709	5.5682
5	1.3248	0.4448	-0.2335	1.4038	0.2785	3.2828	-0.0334	-0.0416	-0.0239	0.0997	0.0453	-0.035	0.5066	-0.1725	-0.0071	0.2832	-0.0388	0.0028	0.2535	-0.0199	0.1967	-10.5629	22	-3.3382
6	0.8185	0.2758	0.2698	0.6489	0.5943	0.4875	0.0786	-0.0909	0.0736	0.0449	-0.2035	0.0959	-0.0152	-0.0505	-0.0078	0.2398	-0.0199	0.0021	0.1915	0.0198	0.1718	-14.2934	14.5917	-26.7829
7	0.6229	0.0559	0.3469	1.9237	-0.531	1.5896	0.0018	0.1681	0.0527	-0.0427	-0.0059	0.0036	0.0519	-0.0581	-0.0003	0.1872	0.028	0.0159	0.1643	0.0248	0.1634	-11.718	11.1179	-37.9414
8	0.5988	0.6419	-0.3012	1.3247	-1.0579	1.9605	-0.0191	0.052	0.1485	-0.0477	0.1556	0.0322	-0.1715	-0.3148	-0	0.2728	0.0135	0.0122	0.288	-0.0077	0.2763	-9.9067	40.4961	-14.3663
9	1.7623	0.176	-0.986	0.1148	-0.4211	1.5948	0.2827	-0.3962	0.4292	0.4315	0.0447	0.2414	-0.3916	0.0219	0.4041	0.2544	-0.0144	-0.0357	0.0696	0.0873	0.1653	-10.7166	37.1855	-35.4943
10	1.188	0.6544	0.3413	2.3057	0.2596	0.3663	0.2532	-0.1251	-0.202	0.7907	-0.1977	-0.4729	0.1646	0.0329	0.031	0.1079	-0.0164	0.0462	0.1979	0.0283	0.1146	-22.9559	19.9635	-44.4546
11	0.9269	0.1947	0.4283	1.2993	-0.0004	1.3009	0.1488	-0.1138	0.0631	0.4565	-0.1088	0.0681	0.1099	-0.1371	0.0057	0.0984	0.0274	0.034	0.1811	0.0429	0.143	-23.1802	21.7944	-44.9549
12	0.7795	-0.4347	-0.0584	1.0911	-0.6569	1.9309	-0.0103	-0.063	-0.0382	0.0372	0.0167	0.0277	0.0859	-0.1989	0.01	0.1153	-0.0195	-0.0041	0.0946	-0.0148	0.1543	-9.9106	-40.4968	-54.587
13	0.2604	0.2159	0.2729	1.3332	0.3233	0.2774	-0.3045	-0.1329	0.0575	0.7297	-0.0115	0.1406	0.1452	-0.5434	-0.0534	0.3149	0.0822	-0.0255	0.2767	-0.0635	0.261	-10.7185	-37.1862	-33.4561
14	0.9312	-0.4197	-0.119	0.4631	0.2413	0.2698	-0.1441	0.069	-0.0856	0.4181	0.0681	0.3548	0.2601	-0.2354	0.0021	0.3145	-0.0167	0.0724	0.2224	-0.0219	0.2512	-22.9667	-19.9646	-24.4992
15	0.753	0.1304	0.0535	1.2462	0.8358	1.2358	-0.264	0.0873	-0.3136	0.4538	-0.0639	0.3776	0.3532	-0.1612	-0.0216	0.2995	0.0082	0.1021	0.213	0.0126	0.2829	-23.1906	-21.7928	-23.9928
16	0.0086	0.0105	-0.0292	0.0254	-0.0438	0.127	0.0612	0.4903	0.1474	0.1264	0.1303	-0.1423	0.1925	0.2825	0.0045	0.1387	0.0022	-0.0015	0.2212	-0.0155	0.1691	-4.3565	-34.6664	-74.5159

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 1 through 100C)	A	1 - 100
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 100D through 134 )	A	100
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 135 through 214 )	A	135 - 214
4	X-RAY DIFFRACTION	4	chain 'G' and (resid 512 through 519 )	G	512 - 519
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 1 through 100C)	H	1 - 100
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 100D through 134 )	H	100
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 135 through 214 )	H	135 - 214
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 1 through 101 )	L	1 - 101
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 102 through 113 )	L	102 - 113
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 114 through 155 )	L	114 - 155
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 156 through 213 )	L	156 - 213
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 101 )	C	1 - 101
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 102 through 113 )	C	102 - 113
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 114 through 155 )	C	114 - 155
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 156 through 213 )	C	156 - 213
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 512 through 519 )	D	512 - 519

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