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- PDB-6w4m: CRYSTAL STRUCTURE OF THE ADCC-POTENT, WEAKLY NEUTRALIZING HIV ENV... -

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Basic information

Entry
Database: PDB / ID: 6w4m
TitleCRYSTAL STRUCTURE OF THE ADCC-POTENT, WEAKLY NEUTRALIZING HIV ENV CO-RECEPTOR BINDING SITE ANTIBODY N12-I2 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 AND M48U1
Components
  • ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN
  • ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN
  • M48U1 CD4 MIMETIC PEPTIDE
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ADCC AND NEUTRALIZING ANTI-HIV-1 ENV ANTIBODY N12-I2 / CD4I ANTIBODY / FAB FRAGMENT / HIV-1 GP120 / IMMUNE SYSTEM / CLADE A/E 93TH057 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120756 United States
CitationJournal: Bmc Biol. / Year: 2020
Title: Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site.
Authors: Tolbert, W.D. / Sherburn, R. / Gohain, N. / Ding, S. / Flinko, R. / Orlandi, C. / Ray, K. / Finzi, A. / Lewis, G.K. / Pazgier, M.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionAug 5, 2020ID: 5UWE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
L: ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN
H: ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN
N: M48U1 CD4 MIMETIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,45713
Polymers91,4664
Non-polymers1,9919
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-37 kcal/mol
Surface area35810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.687, 69.522, 213.468
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 clade A/E 93TH057 HIV-1 gp120 core


Mass: 39160.367 Da / Num. of mol.: 1 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Antibody ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN


Mass: 23437.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN


Mass: 25810.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Protein/peptide M48U1 CD4 MIMETIC PEPTIDE


Mass: 3056.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: 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.: 9
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
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% PEG 6000 5% MPD 0.1 M MES pH 6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.97946
SYNCHROTRONSSRL BL14-120.97946
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJan 7, 2016
MARMOSAIC 325 mm CCD2CCDJan 6, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI (111)SINGLE WAVELENGTHMx-ray1
2SI (111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
21
ReflectionResolution: 3.2→50 Å / Num. obs: 12129 / % possible obs: 88.5 % / Redundancy: 4.3 % / CC1/2: 0.931 / Rmerge(I) obs: 0.321 / Rpim(I) all: 0.156 / Net I/σ(I): 6.3
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 456 / CC1/2: 0.611 / Rpim(I) all: 0.434 / % possible all: 66.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UWE

5uwe
PDB Unreleased entry


Resolution: 3.2→42.34 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65
RfactorNum. reflection% reflection
Rfree0.3011 612 5.06 %
Rwork0.241 --
obs0.2439 12090 88.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6194 0 126 0 6320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036452
X-RAY DIFFRACTIONf_angle_d0.6868759
X-RAY DIFFRACTIONf_dihedral_angle_d16.199924
X-RAY DIFFRACTIONf_chiral_restr0.0471013
X-RAY DIFFRACTIONf_plane_restr0.0051112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.31641260.26722055X-RAY DIFFRACTION65
3.52-4.030.31421650.27453058X-RAY DIFFRACTION96
4.03-5.070.28431560.22753137X-RAY DIFFRACTION97
5.07-42.340.30291650.23033228X-RAY DIFFRACTION95
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)
12.6353-0.9643-0.97432.5678-0.74754.9917-0.2061-0.2032-0.23690.32850.19520.49270.1664-0.39880.09030.39030.0391-0.00120.39560.04040.6509-1.608723.9538-32.6751
23.16211.4032-1.71224.0718-0.79062.7636-0.46620.5654-0.414-1.04930.2176-0.5350.5201-0.07650.14930.7248-0.02220.09720.5004-0.09690.639534.090118.8914-88.2093
32.55811.6545-2.00942.7433-2.32333.3596-0.0290.01080.2065-0.2410.13990.20140.00870.0664-0.09460.5865-0.0448-0.01750.4412-0.0690.560631.554332.0481-76.1671
40.06020.04780.1016-0.14270.0212-0.10240.2767-0.325-1.1054-0.56850.0214-1.02581.08391.4963-00.84650.1209-0.01821.0765-0.01270.998720.502720.4641-33.7932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 47 through 492)
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 212)
3X-RAY DIFFRACTION3(chain 'H' and resid 2 through 216)
4X-RAY DIFFRACTION4(chain 'N' and resid 1 through 27)

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