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- PDB-5cd5: Crystal structure of an immature VRC01-class antibody DRVIA7 from... -

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Entry
Database: PDB / ID: 5cd5
TitleCrystal structure of an immature VRC01-class antibody DRVIA7 from a Chinese donor bound to clade A/E HIV-1 gp120 core
Components
  • 93TH057 HIV-1 gp120 core
  • DRVIA7 Fab Heavy Chain
  • DRVIA7 Fab Light Chain
KeywordsIMMUNE SYSTEM / VRC01 / gp120 / HIV-1 / antibody
Function / homology
Function and homology information


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: 3.396 Å
AuthorsKong, L. / Wilson, I.A.
CitationJournal: Immunity / Year: 2016
Title: Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor.
Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / ...Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / Yanling Hao / Yi Feng / Fernando Garces / Richard Wilson / Kaifan Dai / Sijy O'Dell / Krisha McKee / John R Mascola / Andrew B Ward / Richard T Wyatt / Yuxing Li / Ian A Wilson / Jiang Zhu / Yiming Shao /
Abstract: VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain ...VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain elusive. We demonstrated how VRC01-class antibodies emerged in a Chinese donor by antigen-specific single B cell sorting, structural and functional studies, and longitudinal antibody and virus repertoire analyses. A monoclonal antibody DRVIA7 with modest neutralizing breadth was isolated that displayed a subset of VRC01 signatures. X-ray and EM structures revealed a VRC01-like angle of approach, but less favorable interactions between the DRVIA7 light-chain CDR1 and the N terminus with N276 and V5 glycans of gp120. Although the DRVIA7 lineage was unable to acquire broad neutralization, longitudinal analysis revealed a repertoire-encoded VRC01 light-chain CDR3 signature and VRC01-like neutralizing heavy-chain precursors that rapidly matured within 2 years. Thus, light chain accommodation of the glycan shield should be taken into account in vaccine design targeting this conserved site of vulnerability.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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.name / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 93TH057 HIV-1 gp120 core
C: DRVIA7 Fab Heavy Chain
D: DRVIA7 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,97913
Polymers86,4673
Non-polymers3,51110
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint32 kcal/mol
Surface area35720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.325, 72.325, 338.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 93TH057 HIV-1 gp120 core


Mass: 39211.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: Env / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9*PLUS

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Antibody , 2 types, 2 molecules CD

#2: Antibody DRVIA7 Fab Heavy Chain


Mass: 24048.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Antibody DRVIA7 Fab Light Chain


Mass: 23207.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

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Sugars , 4 types, 10 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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

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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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium iodide and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.39→28.968 Å / Num. obs: 13362 / % possible obs: 99.7 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.31 / Net I/σ(I): 10
Reflection shellResolution: 3.39→3.67 Å / Redundancy: 15.7 % / Rmerge(I) obs: 2.92 / Mean I/σ(I) obs: 1.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.396→28.968 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.306 653 4.93 %
Rwork0.253 --
obs0.2688 13238 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.396→28.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 229 0 6215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066378
X-RAY DIFFRACTIONf_angle_d1.338672
X-RAY DIFFRACTIONf_dihedral_angle_d12.5082317
X-RAY DIFFRACTIONf_chiral_restr0.0981017
X-RAY DIFFRACTIONf_plane_restr0.0121094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.396-3.65720.39751410.37232394X-RAY DIFFRACTION98
3.6572-4.02440.35011420.33112453X-RAY DIFFRACTION100
4.0244-4.60470.2671170.25732478X-RAY DIFFRACTION100
4.6047-5.79390.251290.25882537X-RAY DIFFRACTION100
5.7939-28.9690.32781240.23912723X-RAY DIFFRACTION100
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)
18.3477-0.1336-1.64391.0957-0.38175.26520.27261.21911.1023-0.5547-0.4081-0.4831-0.73140.5109-0.02011.5180.20960.12151.50110.46851.3215118.6591-1.1523-12.7598
28.8889-8.1269-2.40673.73120.03671.56251.22771.75191.33731.6208-1.3494-0.95850.2904-1.003-0.00182.02540.39580.2191.39790.27651.4591100.796913.9133-10.3008
36.2621-0.6206-1.3631.4426-0.35074.96190.09511.445-0.5195-0.8292-0.5363-0.68670.54740.55290.39841.5230.48640.15881.31230.04051.2008112.5794-12.8981-10.3689
46.401-0.35254.44763.1781-8.96495.35330.4041.8185-0.711-1.82280.18150.24930.7188-0.3219-0.44311.97560.3339-0.11331.8205-0.43720.927691.5858-10.3434-11.7595
56.6177-0.69490.31916.60720.9487.0868-0.07310.8496-0.9099-2.3869-0.48111.4543-1.0992-2.22830.66211.46360.1491-0.42962.0735-0.04631.436386.6676-6.9835-13.5031
63.33461.0290.00312.4404-11.56360.2510.85660.03050.2892-0.34950.4943-0.4106-0.14770.06271.64890.4238-0.06961.3245-0.24831.1573102.2621-6.2278-6.6268
71.92562.4856-6.45519.899-3.92151.05841.7702-0.555.33850.7999-0.56892.2056-0.0501-0.1563-0.64191.3920.02870.15320.9023-0.05950.679587.0443-1.932624.2873
810.7656-2.7315-5.11872.23690.46375.28290.39861.6959-0.154-1.0122-0.12760.377-0.2367-1.4452-0.28111.36580.3642-0.19040.9329-0.05040.69191.6544-6.544915.0043
91.53330.454-0.552.0099-0.68712.1464-0.23490.27410.0782-0.2070.1965-0.10780.1785-0.2435-0.05690.9475-0.01620.06310.6205-0.11091.069388.8982-10.604232.0555
107.8734-3.3501-0.7510.5427-0.696311.11570.35010.32551.78121.2306-0.87280.0743-1.49770.26410.49621.4028-0.28560.09830.57650.07281.317679.5845-9.934651.4206
118.27444.11423.47465.50586.098.43290.1021-2.8027-3.4609-1.22260.1535-0.27790.5343-0.8382-0.09921.5492-0.17610.06040.1762-0.17721.206105.0999-26.040432.2957
126.8286-2.14661.02617.7315-3.51756.67250.32420.0769-1.2302-0.4868-0.4647-0.74410.8380.8430.23830.90040.2112-0.020.81620.09741.184109.3697-19.14625.3558
135.13720.2546-0.81931.57180.76366.93171.0672-1.6095-1.4345-1.3408-0.8921-0.56691.3772-0.92990.19661.59760.4230.00580.33890.10871.278104.1836-19.062929.0472
141.80794.1963-6.50432.012-7.05456.47262.1018-0.91531.24591.7879-1.12470.23260.8075-0.37540.28861.7963-0.5190.18291.40880.01371.070799.704-25.957546.8572
155.1935-4.65191.83678.9290.81583.77260.4101-0.2618-0.2629-0.0243-0.55240.7633-0.0960.00120.0551.2096-0.2250.02430.7484-0.04030.984378.2314-24.334249.0505
165.6989-4.5294-0.79046.5514-1.45975.99670.92121.0103-0.61760.2751-0.82911.3168-0.0018-0.5074-0.11231.10850.00210.12030.8931-0.18780.932578.5597-27.858547.6355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 215 )
3X-RAY DIFFRACTION3chain 'A' and (resid 216 through 291 )
4X-RAY DIFFRACTION4chain 'A' and (resid 292 through 395 )
5X-RAY DIFFRACTION5chain 'A' and (resid 396 through 425 )
6X-RAY DIFFRACTION6chain 'A' and (resid 426 through 492 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'C' and (resid 18 through 87 )
9X-RAY DIFFRACTION9chain 'C' and (resid 88 through 133 )
10X-RAY DIFFRACTION10chain 'C' and (resid 134 through 212 )
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 18 )
12X-RAY DIFFRACTION12chain 'D' and (resid 19 through 75 )
13X-RAY DIFFRACTION13chain 'D' and (resid 76 through 102 )
14X-RAY DIFFRACTION14chain 'D' and (resid 103 through 115 )
15X-RAY DIFFRACTION15chain 'D' and (resid 116 through 152 )
16X-RAY DIFFRACTION16chain 'D' and (resid 153 through 213 )

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