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- PDB-5fcu: CRYSTAL STRUCTURE OF THE INNER DOMAIN OF CLADE A/E HIV-1 GP120 IN... -

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Basic information

Entry
Database: PDB / ID: 5fcu
TitleCRYSTAL STRUCTURE OF THE INNER DOMAIN OF CLADE A/E HIV-1 GP120 IN COMPLEX WITH THE ADCC-POTENT RHESUS MACAQUE ANTIBODY JR4
Components
  • JR4 FAB HEAVY CHAIN
  • JR4 FAB LIGHT CHAIN
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 GP120 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGohain, N. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1033109 United States
CitationJournal: Structure / Year: 2016
Title: Paring Down HIV Env: Design and Crystal Structure of a Stabilized Inner Domain of HIV-1 gp120 Displaying a Major ADCC Target of the A32 Region.
Authors: Tolbert, W.D. / Gohain, N. / Veillette, M. / Chapleau, J.P. / Orlandi, C. / Visciano, M.L. / Ebadi, M. / DeVico, A.L. / Fouts, T.R. / Finzi, A. / Lewis, G.K. / Pazgier, M.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Data collection / Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / 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 1.4Sep 27, 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

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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: JR4 FAB HEAVY CHAIN
L: JR4 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,98510
Polymers66,3693
Non-polymers6167
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-80 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.447, 89.848, 180.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-306-

CL

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody JR4 FAB HEAVY CHAIN


Mass: 24847.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human)
#3: Antibody JR4 FAB LIGHT CHAIN


Mass: 22719.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human)

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Protein / Sugars , 2 types, 2 molecules G

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


Mass: 18802.348 Da / Num. of mol.: 1 / Fragment: UNP residues 1-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell line (production host): HEK 293 / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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, 382 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG MONOMETHYL ETHER 5000, 0.2M AMMONIUM SULFATE, 0.1M TRIS-HCL PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014 / Details: RH COATED FLAT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 51569 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 15
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFE

2rfe


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.555 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2617 5.1 %RANDOM
Rwork0.184 ---
obs0.186 48756 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---0.24 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 32 376 4442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194166
X-RAY DIFFRACTIONr_bond_other_d0.0010.023803
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9515686
X-RAY DIFFRACTIONr_angle_other_deg0.89138808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5075525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83224.839155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55515641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1931510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
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_it1.8532.1052124
X-RAY DIFFRACTIONr_mcbond_other1.8512.1042123
X-RAY DIFFRACTIONr_mcangle_it2.8233.1352641
X-RAY DIFFRACTIONr_mcangle_other2.8233.1372642
X-RAY DIFFRACTIONr_scbond_it2.5122.3772042
X-RAY DIFFRACTIONr_scbond_other2.4852.3672031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8333.4373028
X-RAY DIFFRACTIONr_long_range_B_refined6.43820.54617352
X-RAY DIFFRACTIONr_long_range_B_other6.30620.16117029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 180 -
Rwork0.335 3247 -
obs--86.3 %
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)
12.72240.0857-0.05082.1506-3.06056.862-0.0101-0.4103-0.20240.27890.04910.19050.2396-0.1948-0.0390.583-0.0273-0.00030.39750.06760.2142-18.4369-16.663349.4013
21.8549-1.49331.75382.1132-1.20732.31440.091-0.3159-0.15060.17930.10840.340.1076-0.1484-0.19930.0999-0.04560.03770.1511-0.05970.1021-31.93649.525214.6712
31.423-0.85340.1931.5353-0.28140.5498-0.0443-0.23650.1740.29490.0379-0.18950.0213-0.03780.00640.0821-0.0231-0.0320.0507-0.0190.0302-15.897213.659113.6036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G45 - 491
2X-RAY DIFFRACTION2H1 - 213
3X-RAY DIFFRACTION3L2 - 209

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