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- PDB-5wb9: Crystal structure of CD4 binding site antibody N60P23 in complex ... -

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Basic information

Entry
Database: PDB / ID: 5wb9
TitleCrystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 gp120 core
Components
  • N60P23 Fab heavy chain
  • N60P23 Fab light chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN / CD4 binding site / gp120 core
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
AuthorsGohain, N. / Tolbert, W. / Pazgier, M.
CitationJournal: Cell / Year: 2018
Title: Identification of Near-Pan-neutralizing Antibodies against HIV-1 by Deconvolution of Plasma Humoral Responses.
Authors: Sajadi, M.M. / Dashti, A. / Rikhtegaran Tehrani, Z. / Tolbert, W.D. / Seaman, M.S. / Ouyang, X. / Gohain, N. / Pazgier, M. / Kim, D. / Cavet, G. / Yared, J. / Redfield, R.R. / Lewis, G.K. / DeVico, A.L.
History
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: N60P23 Fab heavy chain
L: N60P23 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,84313
Polymers86,7463
Non-polymers2,09710
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint2 kcal/mol
Surface area34140 Å2
Unit cell
Length a, b, c (Å)127.562, 68.567, 119.356
Angle α, β, γ (deg.)90.00, 111.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody N60P23 Fab heavy chain


Mass: 24573.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody N60P23 Fab light chain


Mass: 23011.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 9 molecules G

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


Mass: 39160.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#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.: 8
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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Non-polymers , 3 types, 224 molecules

#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MOPS pH 7.5, ).1M Magnesium acetate hexahydrate
PH range: 6.5-7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 38617 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.7
Reflection shellResolution: 2.38→2.43 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGB

3ngb


Resolution: 2.4→37.33 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 20.788 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25763 1881 5 %RANDOM
Rwork0.21347 ---
obs0.21574 35668 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å2-0.03 Å2
2---0.76 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.4→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5893 0 133 222 6248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196194
X-RAY DIFFRACTIONr_bond_other_d0.0020.025533
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.9628423
X-RAY DIFFRACTIONr_angle_other_deg1.097312935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.875756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05524.672259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.851151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5971526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216761
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9342.0113044
X-RAY DIFFRACTIONr_mcbond_other0.9352.0113043
X-RAY DIFFRACTIONr_mcangle_it1.6113.0093792
X-RAY DIFFRACTIONr_mcangle_other1.6113.0093793
X-RAY DIFFRACTIONr_scbond_it1.3532.2243150
X-RAY DIFFRACTIONr_scbond_other1.3522.2243150
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3573.2944632
X-RAY DIFFRACTIONr_long_range_B_refined6.88639.62226339
X-RAY DIFFRACTIONr_long_range_B_other6.87639.57126285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 130 -
Rwork0.349 2588 -
obs--98.44 %
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)
11.1611-0.26820.80053.0097-0.11773.4037-0.1531-0.14330.04620.4816-0.05320.2936-0.365-0.39110.20620.27210.02650.1240.26-0.04310.106-4.1802-2.000346.3519
21.6224-1.0365-1.97481.63311.73272.7107-0.1059-0.0529-0.15770.134-0.03020.03110.19160.12760.13610.07710.04310.01680.20880.00440.035220.746-24.539214.2733
31.0063-0.9164-0.2773.26091.43911.8060.11010.0267-0.31570.0217-0.21150.25850.1738-0.10030.10140.0479-0.007-0.02510.19810.02920.111211.6138-20.99350.1719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G45 - 492
2X-RAY DIFFRACTION2H1 - 220
3X-RAY DIFFRACTION3L7 - 212

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