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- PDB-4s1q: Crystal structure of a VRC01-lineage antibody, 45-VRC01.H03+06.D-... -

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Basic information

Entry
Database: PDB / ID: 4s1q
TitleCrystal structure of a VRC01-lineage antibody, 45-VRC01.H03+06.D-001739, in complex with clade A/E HIV-1 gp120 core
Components
  • Fab of VRC01 light chain
  • Fab of VRC01-lineage antibody,45-VRC01.H03+06.D-001739 heavy chain
  • HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / neutralizing antibodies / VRC01-lineage / antibody maturation / evolutionary rate / VIRAL PROTEIN-IMMUNE SYSTEM complex
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: 2.4 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 1.2Apr 27, 2016Group: Source and taxonomy
Revision 1.3Jul 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 1.4Jun 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 1.5Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: HIV-1 gp120 core
H: Fab of VRC01-lineage antibody,45-VRC01.H03+06.D-001739 heavy chain
L: Fab of VRC01 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,99914
Polymers87,5663
Non-polymers2,43311
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint11 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.179, 78.925, 194.214
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 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.H03+06.D-001739 heavy chain


Mass: 25264.580 Da / Num. of mol.: 1
Fragment: Fab of VRC01-lineage antibody,45-VRC01.H03+06.D-001739 heavy chain
Source method: isolated from a genetically manipulated source
Details: codon-optimized VRC01-lineage antibody, 45-VRC01.H03+06.D-001739, 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 / N-Acetylglucosamine


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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 8000, 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: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 40685 / Num. obs: 39180 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.113 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.63 / Rsym value: 0.515 / % possible all: 80.4

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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: 2.4→41.355 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 1878 5.08 %
Rwork0.2191 --
obs0.2211 36988 90.47 %
all-40685 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→41.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 154 126 6328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046375
X-RAY DIFFRACTIONf_angle_d0.9568688
X-RAY DIFFRACTIONf_dihedral_angle_d12.3142329
X-RAY DIFFRACTIONf_chiral_restr0.04984
X-RAY DIFFRACTIONf_plane_restr0.0041110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3952-2.460.3387980.28091875X-RAY DIFFRACTION64
2.46-2.53230.35591170.28662210X-RAY DIFFRACTION75
2.5323-2.61410.3431230.28162398X-RAY DIFFRACTION82
2.6141-2.70750.34871360.27762537X-RAY DIFFRACTION86
2.7075-2.81590.35111470.25452698X-RAY DIFFRACTION91
2.8159-2.9440.29191450.25142772X-RAY DIFFRACTION94
2.944-3.09920.2941550.25142834X-RAY DIFFRACTION96
3.0992-3.29320.30181560.24912895X-RAY DIFFRACTION97
3.2932-3.54740.28041560.22642905X-RAY DIFFRACTION98
3.5474-3.90410.25691580.21962938X-RAY DIFFRACTION98
3.9041-4.46850.2141590.18782966X-RAY DIFFRACTION98
4.4685-5.62760.20361610.17462990X-RAY DIFFRACTION98
5.6276-41.36080.24271670.21443092X-RAY DIFFRACTION97

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