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- PDB-5cd3: Structure of immature VRC01-class antibody DRVIA7 -

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Basic information

Entry
Database: PDB / ID: 5cd3
TitleStructure of immature VRC01-class antibody DRVIA7
Components
  • DRVIA7 Heavy Chain
  • DRVIA7 Light Chain
KeywordsIMMUNE SYSTEM / VRC01 / HIV-1 / CD4 binding site / gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 2, 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_CSD / _citation.journal_id_ISSN ..._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_author.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: DRVIA7 Heavy Chain
H: DRVIA7 Light Chain
A: DRVIA7 Heavy Chain
B: DRVIA7 Light Chain
C: DRVIA7 Heavy Chain
D: DRVIA7 Light Chain
E: DRVIA7 Heavy Chain
F: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)189,0248
Polymers189,0248
Non-polymers00
Water00
1
G: DRVIA7 Heavy Chain
H: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area19970 Å2
MethodPISA
2
A: DRVIA7 Heavy Chain
B: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area20010 Å2
MethodPISA
3
C: DRVIA7 Heavy Chain
D: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-24 kcal/mol
Surface area19890 Å2
MethodPISA
4
E: DRVIA7 Heavy Chain
F: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-24 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.829, 73.747, 101.158
Angle α, β, γ (deg.)89.84, 89.40, 89.95
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
DRVIA7 Heavy Chain


Mass: 24048.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody
DRVIA7 Light Chain


Mass: 23207.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.16 M ammonium sulfate, 20% (w/v) PEG 4000, 20% (v/v) glycerol and 0.08 M sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 41586 / % possible obs: 98.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 3.84
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.542 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 2109 5.08 %
Rwork0.2341 --
obs0.2367 41505 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13172 0 0 0 13172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513500
X-RAY DIFFRACTIONf_angle_d1.22618332
X-RAY DIFFRACTIONf_dihedral_angle_d13.6424872
X-RAY DIFFRACTIONf_chiral_restr0.0512052
X-RAY DIFFRACTIONf_plane_restr0.0062348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.96510.35991510.28372443X-RAY DIFFRACTION91
2.9651-3.03920.31381250.28442693X-RAY DIFFRACTION98
3.0392-3.12140.36781460.28552635X-RAY DIFFRACTION98
3.1214-3.21320.29611550.27592670X-RAY DIFFRACTION98
3.2132-3.31690.33411410.27112682X-RAY DIFFRACTION98
3.3169-3.43540.30781310.25962632X-RAY DIFFRACTION98
3.4354-3.57290.33021340.24862678X-RAY DIFFRACTION98
3.5729-3.73550.28671410.25012653X-RAY DIFFRACTION98
3.7355-3.93230.28421280.23122693X-RAY DIFFRACTION98
3.9323-4.17860.26141460.22032638X-RAY DIFFRACTION98
4.1786-4.5010.26421430.19152640X-RAY DIFFRACTION97
4.501-4.95360.23851520.18912616X-RAY DIFFRACTION97
4.9536-5.66950.25551450.20522604X-RAY DIFFRACTION96
5.6695-7.13960.25251290.2392604X-RAY DIFFRACTION95
7.1396-49.54890.24721420.21052515X-RAY DIFFRACTION93

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