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- PDB-7n8q: Rhesusized RV305 DH677.3 Fab bound to Clade A/E 93TH057 HIV-1 gp1... -

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Basic information

Entry
Database: PDB / ID: 7n8q
TitleRhesusized RV305 DH677.3 Fab bound to Clade A/E 93TH057 HIV-1 gp120 core.
Components
  • (Rhesusized DH677.3 FAB ...) x 2
  • M48U1 CD4 MIMETIC PEPTIDE
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / DH677.3 / HIV-1 Env V2 peptide / RV144 / RV305 / Rhesusized antibody
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
Macaca mulatta (Rhesus monkey)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: Front Immunol / Year: 2021
Title: Structure and Fc-Effector Function of Rhesusized Variants of Human Anti-HIV-1 IgG1s.
Authors: Tolbert, W.D. / Nguyen, D.N. / Tuyishime, M. / Crowley, A.R. / Chen, Y. / Jha, S. / Goodman, D. / Bekker, V. / Mudrak, S.V. / DeVico, A.L. / Lewis, G.K. / Theis, J.F. / Pinter, A. / Moody, M. ...Authors: Tolbert, W.D. / Nguyen, D.N. / Tuyishime, M. / Crowley, A.R. / Chen, Y. / Jha, S. / Goodman, D. / Bekker, V. / Mudrak, S.V. / DeVico, A.L. / Lewis, G.K. / Theis, J.F. / Pinter, A. / Moody, M.A. / Easterhoff, D. / Wiehe, K. / Pollara, J. / Saunders, K.O. / Tomaras, G.D. / Ackerman, M. / Ferrari, G. / Pazgier, M.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
N: M48U1 CD4 MIMETIC PEPTIDE
H: Rhesusized DH677.3 FAB HEAVY CHAIN
L: Rhesusized DH677.3 FAB LIGHT CHAIN
A: clade A/E 93TH057 HIV-1 gp120 core
C: Rhesusized DH677.3 FAB HEAVY CHAIN
D: Rhesusized DH677.3 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,33825
Polymers177,3577
Non-polymers3,98218
Water27015
1
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 MIMETIC PEPTIDE
H: Rhesusized DH677.3 FAB HEAVY CHAIN
L: Rhesusized DH677.3 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,19813
Polymers90,2074
Non-polymers1,9919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-0 kcal/mol
Surface area35870 Å2
MethodPISA
2
A: clade A/E 93TH057 HIV-1 gp120 core
C: Rhesusized DH677.3 FAB HEAVY CHAIN
D: Rhesusized DH677.3 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,14112
Polymers87,1503
Non-polymers1,9919
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint3 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.182, 82.664, 111.899
Angle α, β, γ (deg.)90.00, 112.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HCLD

#3: Antibody Rhesusized DH677.3 FAB HEAVY CHAIN


Mass: 24540.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Antibody Rhesusized DH677.3 FAB LIGHT CHAIN


Mass: 23252.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 36 molecules GAN

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


Mass: 39356.613 Da / Num. of mol.: 2 / 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: 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.: 18
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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% PEG 4000 0.1 M sodium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 31091 / % possible obs: 82.7 % / Redundancy: 2.5 % / CC1/2: 0.975 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.078 / Net I/σ(I): 9.6
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1645 / CC1/2: 0.714 / Rpim(I) all: 0.467 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.17.1refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFP

6mfp


Resolution: 2.9→47.93 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.877 / SU B: 74.4 / SU ML: 0.658 / Cross valid method: THROUGHOUT / ESU R Free: 0.594 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29578 1599 5.1 %RANDOM
Rwork0.25517 ---
obs0.2572 29478 82.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.955 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å2-1.3 Å2
2---0.66 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 2.9→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 252 15 12057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312345
X-RAY DIFFRACTIONr_bond_other_d0.0040.01711047
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6816808
X-RAY DIFFRACTIONr_angle_other_deg1.5231.60125835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4851507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96224.048541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.357151987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.91539
X-RAY DIFFRACTIONr_chiral_restr0.0870.21709
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213563
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022385
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_it3.8164.0186096
X-RAY DIFFRACTIONr_mcbond_other3.8164.0186095
X-RAY DIFFRACTIONr_mcangle_it6.0836.0077576
X-RAY DIFFRACTIONr_mcangle_other6.0836.0077577
X-RAY DIFFRACTIONr_scbond_it4.0894.2626249
X-RAY DIFFRACTIONr_scbond_other4.0894.2626247
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2396.3119232
X-RAY DIFFRACTIONr_long_range_B_refined10.79275.61548382
X-RAY DIFFRACTIONr_long_range_B_other10.79275.61448377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.973 Å
RfactorNum. reflection% reflection
Rfree0.394 142 -
Rwork0.378 2234 -
obs--85.47 %
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)
10.3877-0.19440.30960.1614-0.05830.8193-0.00630.03490.01940.04890.04540.0373-0.110.1399-0.03910.5122-0.0566-0.06180.3579-0.06770.2018-16.147511.73212.7075
20.10070.06270.1540.30490.23320.5842-0.0780.078-0.0887-0.00060.05870.0532-0.10040.13540.01930.54040.0237-0.0430.3738-0.05020.19616.109413.770859.2205
30.05150.0360.11290.35110.7161.52150.0354-0.1013-0.0053-0.0007-0.03850.01820.0151-0.10710.00310.5774-0.0114-0.12740.2702-0.03880.05091.55229.255568.5595
40.71690.25350.28550.12770.04660.7807-0.0838-0.0911-0.1187-0.030.0094-0.0517-0.0092-0.00350.07440.54330.0524-0.16150.3419-0.06360.1197-9.325-29.816325.2834
50.2259-0.1592-0.17850.3151-0.0030.49980.08640.01360.0456-0.0029-0.0310.0845-0.10340.1422-0.05540.5049-0.0288-0.09660.3837-0.03980.145823.1179-21.947569.8647
60.0877-0.07080.13380.46070.4941.27690.0586-0.02010.00330.02420.0634-0.00990.0667-0.0717-0.1220.4852-0.0509-0.08310.3544-0.01330.231210.8045-30.021880.2992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G1 - 492
2X-RAY DIFFRACTION2H1 - 215
3X-RAY DIFFRACTION3L1 - 214
4X-RAY DIFFRACTION4A1 - 492
5X-RAY DIFFRACTION5C1 - 215
6X-RAY DIFFRACTION6D1 - 214

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