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- PDB-5f6j: Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rh... -

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Basic information

Entry
Database: PDB / ID: 5f6j
TitleCrystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque in Complex with HIV-1 gp120 Core
Components
  • DH427 Antibody Heavy Chain
  • DH427 Antibody Light Chain
  • ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
KeywordsViral Protein/Immue System / FAB FRAGMENT / HIV-1 / ANTIBODY / Viral Protein-Immue System complex
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.63 Å
AuthorsFera, D. / Harrison, S.C.
CitationJournal: Cell Rep / Year: 2016
Title: Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site.
Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. ...Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. / Foulger, A. / Nie, X. / Karim, S.S. / Barnett, S. / Kelsoe, G. / Kepler, T.B. / Alam, S.M. / Montefiori, D.C. / Moody, M.A. / Liao, H.X. / Morris, L. / Santra, S. / Harrison, S.C. / Haynes, B.F.
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
E: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
A: DH427 Antibody Light Chain
B: DH427 Antibody Heavy Chain
F: DH427 Antibody Light Chain
H: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)172,5296
Polymers172,5296
Non-polymers00
Water00
1
G: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
A: DH427 Antibody Light Chain
B: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)86,2653
Polymers86,2653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
F: DH427 Antibody Light Chain
H: DH427 Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)86,2653
Polymers86,2653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.902, 162.902, 229.854
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21E
12A
22F
13B
23H

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSGA44 - 4921 - 352
21VALVALLYSLYSEB44 - 4921 - 352
12SERSERTHRTHRAC2 - 2132 - 213
22SERSERTHRTHRFE2 - 2132 - 213
13GLUGLUPROPROBD1 - 2171 - 217
23GLUGLUPROPROHF1 - 2171 - 217

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.792635, -0.608654, 0.035638), (-0.609309, -0.79286, 0.010735), (0.021722, -0.030223, -0.999307)-71.578697, -203.712463, 78.934143
3given(1), (1), (1)
4given(0.764619, -0.64439, 0.010913), (-0.644322, -0.763942, 0.035253), (-0.01438, -0.033987, -0.999319)-72.672859, -196.119934, 82.645493
5given(1), (1), (1)
6given(0.765518, -0.642399, 0.036144), (-0.643242, -0.765405, 0.01986), (0.014907, -0.038452, -0.999149)-74.698868, -195.436493, 78.163811

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Components

#1: Protein ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C


Mass: 39031.199 Da / Num. of mol.: 2 / Mutation: G321K, N326S, D327N, 322-324 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) / References: UniProt: R4GRV3
#2: Antibody DH427 Antibody Light Chain


Mass: 22858.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Antibody DH427 Antibody Heavy Chain


Mass: 24375.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / 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: 5.1 Å3/Da / Density % sol: 75.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5M ammonium sulfate and 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 6.63→141.08 Å / Num. obs: 6058 / % possible obs: 93.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.273 / Rpim(I) all: 0.146 / Rrim(I) all: 0.312 / Χ2: 1.197 / Net I/av σ(I): 6.615 / Net I/σ(I): 7.5 / Num. measured all: 78988
Reflection shellResolution: 6.63→6.8 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.1 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H

4lst

5f6h


Resolution: 6.63→141.08 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2767 / WRfactor Rwork: 0.2337 / FOM work R set: 0.6853 / SU B: 381.586 / SU ML: 2.969 / SU Rfree: 2.9795 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 2.98 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3046 302 5 %RANDOM
Rwork0.256 ---
obs0.2585 5756 93.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 480 Å2 / Biso mean: 276.625 Å2 / Biso min: 130.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0.71 Å20 Å2
2---1.41 Å20 Å2
3---4.59 Å2
Refinement stepCycle: final / Resolution: 6.63→141.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11572 0 0 0 11572
Num. residues----1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911852
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.94516124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45751500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34824.596470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.676151926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7461546
X-RAY DIFFRACTIONr_chiral_restr0.0840.21830
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218832
X-RAY DIFFRACTIONr_mcbond_it9.97927.2616048
X-RAY DIFFRACTIONr_mcangle_it17.61540.8797531
X-RAY DIFFRACTIONr_scbond_it9.75728.1015804
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1G264034.68
2A157418.53
3B157216.94
LS refinement shellResolution: 6.625→6.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 26 -
Rwork0.356 415 -
all-441 -
obs--91.68 %

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