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- PDB-4s1r: Crystal structure of a VRC01-lineage antibody, 45-VRC01.H08.F-117... -

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Basic information

Entry
Database: PDB / ID: 4s1r
TitleCrystal structure of a VRC01-lineage antibody, 45-VRC01.H08.F-117225, in complex with clade A/E HIV-1 gp120 core
Components
  • Fab of VRC01 light chain
  • Fab of VRC01-lineage antibody,45-VRC01.H08.F-117225 heavy chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM/INHIBITOR / HIV-1 / neutralizing antibodies / VRC01-lineage / antibody maturation / evolutionary rate / VIRAL PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.214 Å
AuthorsKwon, Y.D. / Yang, Y. / Zhang, B. / Kwong, P.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2015
Title: Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.
Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / ...Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / Saunders, K.O. / Soto, C. / Srivatsan, S. / Yang, Y. / Bailer, R.T. / Louder, M.K. / Mullikin, J.C. / Connors, M. / Kwong, P.D. / Mascola, J.R. / Shapiro, L.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: 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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 20, 2023Group: 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: Fab of VRC01-lineage antibody,45-VRC01.H08.F-117225 heavy chain
L: Fab of VRC01 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,85214
Polymers87,4183
Non-polymers2,43311
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint22 kcal/mol
Surface area36830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.685, 68.196, 204.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: residue 44-492 / Mutation: V1V2 and V3 deletion
Source method: isolated from a genetically manipulated source
Details: HIV-1 gp120 core / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: clade A/E 93TH057 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9*PLUS
#2: Antibody Fab of VRC01-lineage antibody,45-VRC01.H08.F-117225 heavy chain


Mass: 25117.328 Da / Num. of mol.: 1
Fragment: Fab of VRC01-lineage antibody,45-VRC01.H08.F-117225 heavy chain
Source method: isolated from a genetically manipulated source
Details: codon-optimized VRC01-lineage antibody, 45-VRC01.H08.F-117225, heavy chain
Source: (gene. exp.) Homo sapiens (human) / Gene: Heavy chain / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Fab of VRC01 light chain


Mass: 23089.572 Da / Num. of mol.: 1 / Fragment: Fab of VRC01 light chain / Mutation: N72T
Source method: isolated from a genetically manipulated source
Details: codon-optimized human antibody VRC01 light chain / Source: (gene. exp.) Homo sapiens (human) / Gene: Light chain / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#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.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 4000, 0.1M NaAcetate, 0.1M Tris-HCl, 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 15616 / Num. obs: 14617 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 88 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.156 / Net I/σ(I): 8.78
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 1.62 / Rsym value: 0.53 / % possible all: 53.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE8

3se8


Resolution: 3.214→48.165 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 32.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2861 664 4.56 %
Rwork0.2608 --
obs0.2621 14552 93.23 %
all-15608 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.214→48.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6019 0 154 0 6173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056337
X-RAY DIFFRACTIONf_angle_d1.078632
X-RAY DIFFRACTIONf_dihedral_angle_d11.5332321
X-RAY DIFFRACTIONf_chiral_restr0.077982
X-RAY DIFFRACTIONf_plane_restr0.0041104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2137-3.46170.3424840.33652077X-RAY DIFFRACTION71
3.4617-3.810.36321350.30362824X-RAY DIFFRACTION96
3.81-4.3610.28221480.27462917X-RAY DIFFRACTION99
4.361-5.49310.25171200.24182991X-RAY DIFFRACTION100
5.4931-48.17010.27421770.23923079X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.8531.90090.87043.4874-0.80930.53030.2510.16010.85840.1538-0.40830.39820.11190.44150.20940.6510.01690.19530.604-0.02280.706316.637.1494-44.4995
23.75543.53612.37035.88692.77832.82490.5642-0.47612.12680.2128-0.90582.29760.5398-1.15590.19730.5847-0.08160.01390.8080.05791.0311-0.5167-4.0403-46.579
32.89142.03291.74595.04211.44474.588-0.50690.22370.26840.10980.19320.102-0.75750.69850.23360.5613-0.03280.12810.42270.02680.608915.96910.3629-44.7401
42.69240.11150.53562.9991-1.07654.98660.01470.33070.0068-0.1192-0.2688-0.25450.58650.61670.15180.61640.09420.090.4418-0.02260.516420.8314-19.3845-43.9846
53.96631.3170.50773.36550.30924.2835-0.067-0.4069-0.3289-0.0728-0.0037-0.04921.7871-0.04690.03940.66660.20490.01990.3553-0.00950.56049.9876-21.0787-50.4953
65.8181-1.43831.78342.6705-0.74360.60491.1788-1.3876-0.1248-0.8093-0.20140.13170.076-0.0102-0.57691.1109-0.02980.10840.7531-0.03060.513619.1609-29.0107-52.4436
77.05372.6805-0.43924.1152-0.7773.59510.28670.32171.152-0.64350.01450.5817-0.5031-0.5983-0.22060.56570.0888-0.12390.64780.020.8113-1.7868-14.8113-54.0243
86.13890.73651.14172.53871.51127.4089-0.7379-0.385-0.1832-0.2127-0.3025-1.53131.0762-0.2126-0.55520.8112-0.01120.26540.4095-0.06390.381917.6699-22.2036-38.8939
96.57091.7287-1.31086.06510.075.14120.0488-0.1955-0.55460.60180.23640.2346-0.21150.1234-0.46390.50320.0877-0.0410.46710.12720.523815.5904-0.6182-37.8861
105.73492.9928-1.00055.6783-0.88646.15050.3932-0.1457-0.08650.3529-0.29380.38980.4642-0.076-0.09110.5331-0.05290.0870.4313-0.04570.4735-1.3115-26.7757-25.4778
112.11060.0156-1.42461.6123-1.30741.7038-0.16940.2056-0.1822-0.1624-0.12140.28450.3375-0.0150.18690.875-0.26060.11160.6682-0.24210.6488-6.7788-27.5682-13.9974
126.115-1.92211.37644.24631.41672.0449-0.42250.7676-1.1043-1.05680.67950.8197-0.20690.06340.01731.2109-0.33910.18331.4039-0.20480.984-21.9288-41.53620.7021
133.46970.09960.10064.3546-0.27913.66680.2337-1.62140.31061.7838-0.3362-0.31070.44040.28170.26231.2055-0.0575-0.07621.0563-0.09090.710912.2991-22.950.3247
142.39960.18482.51816.3378-2.19986.3633-0.4578-0.51530.55210.26640.0168-0.043-0.5361-0.33590.40870.9466-0.15240.26160.7342-0.18740.61527.5897-15.6048-5.2333
152.5679-0.701-2.71672.3881-3.28077.85560.13160.0135-0.08040.5221-0.0248-0.1533-1.07460.0321-0.18441.0355-0.0940.12380.5788-0.05070.72864.2015-26.92880.1648
169.6534-5.61385.05583.8729-3.42733.00531.92411.3083-2.37712.34613.28110.22620.33851.70111.73051.7617-0.08880.64951.5345-0.80622.0531-16.0988-52.94673.5921
170.1593-0.39090.66582.0007-5.10674.0955-1.3753-1.7971-2.98191.8207-0.1911-0.22380.11130.3844-0.54590.22820.34270.76271.8244-0.06662.4502-2.8244-46.8139.6753
182.98760.99332.07831.04540.4195.76410.63250.9625-0.51863.06210.4958-0.80610.6427-0.1223-0.30591.0501-0.04140.48750.80050.18661.3219-8.946-45.12174.7728
190.3255-0.09460.87511.32680.25762.6697-1.0244-1.5126-1.06070.183-0.41171.10340.10470.0460.17640.88680.06110.66821.4719-0.21612.4103-4.8484-50.703213.4563
202.2112-0.8961-0.30832.14990.41143.5793-0.1794-1.9085-1.2452-0.19730.30311.38420.4454-1.7455-0.41571.8365-0.08370.17191.33250.26491.7492-9.7733-54.008617.0492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND RESID 44:98 )G44 - 98
2X-RAY DIFFRACTION2( CHAIN G AND RESID 99:200 )G99 - 200
3X-RAY DIFFRACTION3( CHAIN G AND RESID 201:258 )G201 - 258
4X-RAY DIFFRACTION4( CHAIN G AND RESID 259:368 )G259 - 368
5X-RAY DIFFRACTION5( CHAIN G AND RESID 369:393 )G369 - 393
6X-RAY DIFFRACTION6( CHAIN G AND RESID 394:421 )G394 - 421
7X-RAY DIFFRACTION7( CHAIN G AND RESID 422:442 )G422 - 442
8X-RAY DIFFRACTION8( CHAIN G AND RESID 443:470 )G443 - 470
9X-RAY DIFFRACTION9( CHAIN G AND RESID 471:492 )G471 - 492
10X-RAY DIFFRACTION10( CHAIN H AND RESID 1:99 )H1 - 99
11X-RAY DIFFRACTION11( CHAIN H AND RESID 100:153 )H100 - 153
12X-RAY DIFFRACTION12( CHAIN H AND RESID 154:216 )H154 - 216
13X-RAY DIFFRACTION13( CHAIN L AND RESID 3:25 )L3 - 25
14X-RAY DIFFRACTION14( CHAIN L AND RESID 26:83 )L26 - 83
15X-RAY DIFFRACTION15( CHAIN L AND RESID 84:117 )L84 - 117
16X-RAY DIFFRACTION16( CHAIN L AND RESID 118:138 )L118 - 138
17X-RAY DIFFRACTION17( CHAIN L AND RESID 139:160 )L139 - 160
18X-RAY DIFFRACTION18( CHAIN L AND RESID 161:191 )L161 - 191
19X-RAY DIFFRACTION19( CHAIN L AND RESID 192:201 )L192 - 201
20X-RAY DIFFRACTION20( CHAIN L AND RESID 202:216 )L202 - 216

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