PDB-4r4b: Crystal structure of the anti-hiv-1 antibody 2.2c

ID or keywords:

Entry

Database: PDB / ID: 4r4b

Title

Crystal structure of the anti-hiv-1 antibody 2.2c

Components

FAB 2.2C HEAVY CHAIN
FAB 2.2C LIGHT CHAIN

Keywords

IMMUNE SYSTEM / IGG / FAB / HIV / IMMUNOGLOBULIN DOMAIN

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.199 Å

Authors

McLellan, J.S. / Acharya, P. / Huang, C.-C. / Robinson, J. / Kwong, P.D.

Citation

Journal: J.Virol. / Year: 2014
Title: Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection.
Authors: Acharya, P. / Tolbert, W.D. / Gohain, N. / Wu, X. / Yu, L. / Liu, T. / Huang, W. / Huang, C.C. / Kwon, Y.D. / Louder, R.K. / Luongo, T.S. / McLellan, J.S. / Pancera, M. / Yang, Y. / Zhang, B. ...

History

Deposition	Aug 19, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2014	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Jan 10, 2024	Group: Derived calculations / Category: struct_conn

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4r4b.cif.gz	678.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4r4b.ent.gz	563.1 KB	Display	PDB format
PDBx/mmJSON format	4r4b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4r4b_validation.pdf.gz	522.2 KB	Display	wwPDB validaton report
Full document	4r4b_full_validation.pdf.gz	539.4 KB	Display
Data in XML	4r4b_validation.xml.gz	73.5 KB	Display
Data in CIF	4r4b_validation.cif.gz	103.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r4/4r4b ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r4b	HTTPS FTP

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Related structure data

Related structure data	4h8wC 4r4fC 4r4hC 4r4nC 1u6aS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3hi5-d 2fjf-10 5i8c-d 2fjf-5 4why-4 1kcu-d 4wht-9 3nab-d 3cfe-2 6gc2-d 7lk9-1 6oed-1 7lk9-3 1dqq-1 1xf3-1 6pxr-d 4ocx-d 3piq-2 4py7-2 5ty6-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

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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

L: FAB 2.2C LIGHT CHAIN

H: FAB 2.2C HEAVY CHAIN

A: FAB 2.2C LIGHT CHAIN

B: FAB 2.2C HEAVY CHAIN

C: FAB 2.2C LIGHT CHAIN

D: FAB 2.2C HEAVY CHAIN

E: FAB 2.2C LIGHT CHAIN

F: FAB 2.2C HEAVY CHAIN

hetero molecules

191 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: FAB 2.2C LIGHT CHAIN

H: FAB 2.2C HEAVY CHAIN

hetero molecules

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

2

A: FAB 2.2C LIGHT CHAIN

B: FAB 2.2C HEAVY CHAIN

hetero molecules

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

3

C: FAB 2.2C LIGHT CHAIN

D: FAB 2.2C HEAVY CHAIN

hetero molecules

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

4

E: FAB 2.2C LIGHT CHAIN

F: FAB 2.2C HEAVY CHAIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	195.011, 133.559, 90.774
Angle α, β, γ (deg.)	90.00, 91.36, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	L-304- SO4
2	1	L-482- HOH

#1: Antibody

FAB 2.2C LIGHT CHAIN

Mass: 22912.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): HYBRIDOMA / Production host:

Homo sapiens (human)

#2: Antibody

FAB 2.2C HEAVY CHAIN

Mass: 23704.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): HYBRIDOMA / Production host:

Homo sapiens (human)

#3: Chemical

...
ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: SO₄

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1233 / 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: 3.17 Å³/Da / Density % sol: 61.18 %
Crystal grow	pH: 4.5 Details: 100 MM NAOAC PH 4.5, 0-2 % V/V ISOPROPANOL, 2 M LI2SO4, 100 MM MGSO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.199→50 Å / Num. obs: 110015 / % possible obs: 93.6 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / R_sym value: 0.09 / Net I/σ(I): 12.6
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 2.3 % / R_sym value: 0.4 / % possible all: 67.8

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Processing

Software

Name	Version	Classification
MOLREP		phasing
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1U6A

1u6a

Resolution: 2.199→48.662 Å / SU ML: 0.24 / σ(F): 1 / Phase error: 22.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2144	5221	5.02 %
R_work	0.1655	-	-
obs	0.1679	103915	88.2 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.199→48.662 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13054	0	236	1233	14523

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	13602
X-RAY DIFFRACTION	f_angle_d	0.897	18528
X-RAY DIFFRACTION	f_dihedral_angle_d	12.46	4812
X-RAY DIFFRACTION	f_chiral_restr	0.032	2080
X-RAY DIFFRACTION	f_plane_restr	0.004	2322

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 (%)
2.1991-2.2241	0.2751	101	0.219	1787	X-RAY DIFFRACTION	48
2.2241-2.2503	0.2764	117	0.2215	2164	X-RAY DIFFRACTION	59
2.2503-2.2777	0.3064	111	0.214	2282	X-RAY DIFFRACTION	61
2.2777-2.3066	0.2756	128	0.2212	2425	X-RAY DIFFRACTION	65
2.3066-2.3369	0.3007	130	0.212	2504	X-RAY DIFFRACTION	68
2.3369-2.3689	0.2634	160	0.2092	2712	X-RAY DIFFRACTION	73
2.3689-2.4028	0.2937	139	0.211	2845	X-RAY DIFFRACTION	77
2.4028-2.4386	0.274	163	0.2051	2966	X-RAY DIFFRACTION	80
2.4386-2.4767	0.2668	181	0.2131	3107	X-RAY DIFFRACTION	84
2.4767-2.5173	0.2693	162	0.2114	3294	X-RAY DIFFRACTION	88
2.5173-2.5607	0.2681	175	0.2075	3340	X-RAY DIFFRACTION	90
2.5607-2.6073	0.2998	188	0.2084	3416	X-RAY DIFFRACTION	92
2.6073-2.6574	0.2541	209	0.2016	3419	X-RAY DIFFRACTION	93
2.6574-2.7117	0.2605	180	0.203	3503	X-RAY DIFFRACTION	94
2.7117-2.7706	0.255	201	0.1935	3543	X-RAY DIFFRACTION	96
2.7706-2.8351	0.2458	212	0.1908	3591	X-RAY DIFFRACTION	96
2.8351-2.906	0.2564	203	0.1875	3533	X-RAY DIFFRACTION	96
2.906-2.9845	0.2552	190	0.1839	3598	X-RAY DIFFRACTION	97
2.9845-3.0723	0.2091	202	0.1789	3691	X-RAY DIFFRACTION	98
3.0723-3.1715	0.2169	183	0.1753	3668	X-RAY DIFFRACTION	98
3.1715-3.2848	0.2088	200	0.162	3679	X-RAY DIFFRACTION	98
3.2848-3.4163	0.2024	192	0.1537	3667	X-RAY DIFFRACTION	99
3.4163-3.5717	0.1881	199	0.148	3701	X-RAY DIFFRACTION	99
3.5717-3.76	0.2118	190	0.1447	3747	X-RAY DIFFRACTION	100
3.76-3.9955	0.2015	162	0.1381	3727	X-RAY DIFFRACTION	99
3.9955-4.3038	0.1468	183	0.1205	3724	X-RAY DIFFRACTION	99
4.3038-4.7366	0.1341	174	0.1103	3773	X-RAY DIFFRACTION	100
4.7366-5.4212	0.1591	187	0.1267	3744	X-RAY DIFFRACTION	100
5.4212-6.8271	0.2079	189	0.1692	3749	X-RAY DIFFRACTION	100
6.8271-48.6738	0.2119	210	0.191	3795	X-RAY DIFFRACTION	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	1.0863	-0.4193	-0.2784	0.608	0.0471	0.6822	0.0071	-0.0216	-0.1756	-0.0557	-0.0201	0.1595	-0.1067	-0.0468	0.0002	0.1367	0.009	0.0008	0.1124	0.0091	0.1698	11.2187	5.0522	-8.1012
2	0.3395	0.0146	-0.0248	0.4487	-0.3249	1.2886	-0.1106	0.0454	-0.0008	0.1198	0.0208	-0.0079	-0.2186	-0.0358	-0.1052	0.2171	0.0079	-0.0178	0.1984	0.0035	0.1006	9.5922	33.2414	-30.1418
3	0.5767	-0.0241	-0.2363	0.8319	-0.4609	0.517	0.0414	0.0394	-0.0792	-0.091	-0.0252	0.0393	0.0345	0.0454	-0	0.1503	0.0412	-0.004	0.1325	-0.0024	0.1478	28.25	-1.3927	-21.2138
4	0.2291	0.0887	0.1853	0.4316	-0.5859	1.0755	-0.0557	0.0482	0.127	0.157	0.028	-0.1661	-0.0778	0.28	0	0.2371	-0.025	-0.0643	0.2852	-0.0287	0.2134	24.9495	34.2101	-26.9994
5	0.7134	-0.8986	0.5594	1.0628	0.007	1.0075	0.0542	-0.0329	0.1306	0.1102	-0.1134	-0.0327	0.0691	0.0289	0.0001	0.1496	-0.0215	0.029	0.1604	-0.0022	0.13	88.0433	-22.9233	-6.3429
6	0.721	-0.2668	0.3734	-0.1633	-1.0158	1.5585	0.1417	0.0605	-0.1043	-0.027	-0.0543	-0	0.3114	0.2297	0.002	0.2629	0.0262	-0.0181	0.1993	-0.0319	0.1353	87.3162	-51.4373	-29.026
7	0.7763	-0.1694	0.3587	0.8801	0.4156	0.8876	0.033	0.1137	0.0901	-0.0743	-0.1028	0.085	-0.0302	0.0132	-0.0791	0.169	0.0441	0.0129	0.1634	-0.0189	0.1407	72.2703	-15.1691	-20.2913
8	0.3912	0.245	0.5089	0.6539	0.991	1.5509	0.1435	-0.1577	0.0213	-0.0471	-0.1633	0.1331	0.3363	-0.4541	-0.0165	0.2173	-0.0624	0.015	0.2845	0.0074	0.1229	71.9923	-49.3635	-26.5756
9	0.7476	0.4455	-0.0056	0.5616	-0.0829	0.4948	0.0153	-0.3406	-0.0058	0.0707	0.1269	-0.0994	0.128	-0	0.0011	0.1962	0.048	-0.0396	0.3064	0.0308	0.2234	50.7388	-23.8657	11.8066
10	0.8524	-0.2084	-0.2793	0.1825	0.2886	1.1612	-0.0085	-0.7406	0.093	0.2257	0.0345	0.2221	0.2348	-0.1568	0.1249	0.3399	-0.0233	0.1112	0.5788	0.164	0.4361	15.7211	-26.2724	21.9303
11	0.8072	0.1556	0.0818	0.8603	0.1057	0.4213	0.0579	-0.0294	-0.1322	-0.1061	-0.0092	0.0177	0.0241	0.0451	0.0138	0.1461	0.0079	-0.0141	0.1277	0.0283	0.2357	42.529	-26.8467	-8.6835
12	1.1918	0.0361	0.2897	0.4962	-0.4335	0.5397	-0.1037	-0.2073	-0.0754	0.1347	0.09	0.113	0.0073	-0.0972	-0	0.214	0.0427	0.0429	0.1664	0.0476	0.3127	16.2038	-18.3741	8.1433
13	0.8667	0.5319	-0.0868	0.587	0.0153	0.9719	-0.1265	-0.3356	-0.0596	0.0833	0.0837	-0.0051	-0.2089	-0.0808	-0.0055	0.1781	0.0976	0.0261	0.2896	-0.0031	0.1746	47.9869	6.0142	12.2015
14	0.5277	-0.2729	0.2519	0.3721	-0.5882	0.6594	-0.2377	-1.183	-0.3265	0.3128	0.304	-0.341	-0.0741	0.3409	0.1665	0.3783	0.043	-0.1977	0.9485	-0.3686	0.5009	82.5528	8.5263	23.9512
15	1.3958	-0.5435	-0.0451	0.8174	-0.1516	0.0189	0.0581	-0.0208	0.1306	-0.0897	0.0075	-0.2028	-0.087	-0.0772	0.136	0.1907	0.0008	0.0367	0.124	-0.0283	0.2505	57.3669	9.6941	-7.5546
16	1.3924	-0.0913	-0.114	0.5164	0.3358	0.6303	-0.1858	-0.4464	0.1643	-0.0611	0.1828	-0.2722	0.0146	0.1991	0.0135	0.2032	0.0772	-0.0486	0.3133	-0.0954	0.3179	82.7612	0.7573	10.1029

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain L and resid 1:107
2	X-RAY DIFFRACTION	2	chain L and resid 109:211
3	X-RAY DIFFRACTION	3	chain H and resid 1:118
4	X-RAY DIFFRACTION	4	chain H and resid 123:214
5	X-RAY DIFFRACTION	5	chain A and resid 1:107
6	X-RAY DIFFRACTION	6	chain A and resid 109:211
7	X-RAY DIFFRACTION	7	chain B and resid 1:118
8	X-RAY DIFFRACTION	8	chain B and resid 123:214
9	X-RAY DIFFRACTION	9	chain C and resid 1:107
10	X-RAY DIFFRACTION	10	chain C and resid 109:211
11	X-RAY DIFFRACTION	11	chain D and resid 1:118
12	X-RAY DIFFRACTION	12	chain D and resid 123:214
13	X-RAY DIFFRACTION	13	chain E and resid 1:107
14	X-RAY DIFFRACTION	14	chain E and resid 109:211
15	X-RAY DIFFRACTION	15	chain F and resid 1:118
16	X-RAY DIFFRACTION	16	chain F and resid 123:214

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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

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Mar 5, 2020. Novel coronavirus structure data

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Jul 12, 2017. Major update of PDB

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Yorodumi