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- PDB-6mnq: Rhesus macaque anti-HIV V3 antibody DH727.2 with gp120 V3 ZAM18 p... -

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Basic information

Entry
Database: PDB / ID: 6mnq
TitleRhesus macaque anti-HIV V3 antibody DH727.2 with gp120 V3 ZAM18 peptide
Components
  • Ab DH727.2 heavy chain Fab fragment
  • Ab DH727.2 light chain
  • Envelope glycoprotein
KeywordsIMMUNE SYSTEM / HIV-1 gp120 V3 antibody
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / viral envelope / Immunoglobulin-like / Sandwich / Mainly Beta / Envelope glycoprotein
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsNicely, N.I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI120801 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1-AI100645 United States
CitationJournal: Nat Commun / Year: 2019
Title: Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations.
Authors: Han, Q. / Jones, J.A. / Nicely, N.I. / Reed, R.K. / Shen, X. / Mansouri, K. / Louder, M. / Trama, A.M. / Alam, S.M. / Edwards, R.J. / Bonsignori, M. / Tomaras, G.D. / Korber, B. / ...Authors: Han, Q. / Jones, J.A. / Nicely, N.I. / Reed, R.K. / Shen, X. / Mansouri, K. / Louder, M. / Trama, A.M. / Alam, S.M. / Edwards, R.J. / Bonsignori, M. / Tomaras, G.D. / Korber, B. / Montefiori, D.C. / Mascola, J.R. / Seaman, M.S. / Haynes, B.F. / Saunders, K.O.
History
DepositionOct 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Envelope glycoprotein
H: Ab DH727.2 heavy chain Fab fragment
L: Ab DH727.2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0016
Polymers49,8153
Non-polymers1863
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-20 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.511, 95.780, 58.049
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Envelope glycoprotein


Mass: 2394.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A0A0K0KAD3
#2: Antibody Ab DH727.2 heavy chain Fab fragment


Mass: 23385.338 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 Ab DH727.2 light chain


Mass: 24034.498 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)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 20% PEG 6,000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41285 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rpim(I) all: 0.067 / Rsym value: 0.113 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2038 / Rpim(I) all: 0.401 / Rsym value: 0.69 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4HCR

4hcr


Resolution: 1.804→28.993 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.53
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1993 4.83 %Random selection
Rwork0.1846 ---
obs0.1865 41254 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.804→28.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 12 257 3612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083441
X-RAY DIFFRACTIONf_angle_d1.2044678
X-RAY DIFFRACTIONf_dihedral_angle_d13.8961234
X-RAY DIFFRACTIONf_chiral_restr0.048538
X-RAY DIFFRACTIONf_plane_restr0.006599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8037-1.84880.24881250.20742601X-RAY DIFFRACTION93
1.8488-1.89870.25881570.21082836X-RAY DIFFRACTION100
1.8987-1.95460.24751280.20332823X-RAY DIFFRACTION100
1.9546-2.01770.25971540.20072816X-RAY DIFFRACTION100
2.0177-2.08980.24781330.19772861X-RAY DIFFRACTION100
2.0898-2.17340.2311500.19812811X-RAY DIFFRACTION100
2.1734-2.27230.26951470.19612800X-RAY DIFFRACTION100
2.2723-2.3920.25911360.19622826X-RAY DIFFRACTION100
2.392-2.54180.22561470.21012821X-RAY DIFFRACTION100
2.5418-2.7380.24971420.20772819X-RAY DIFFRACTION99
2.738-3.01320.27321360.2092821X-RAY DIFFRACTION99
3.0132-3.44860.22961510.18472811X-RAY DIFFRACTION99
3.4486-4.34260.17641450.15622819X-RAY DIFFRACTION99
4.3426-28.99670.18051420.15052796X-RAY DIFFRACTION97
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)
12.4536-0.50050.65363.12821.27552.2637-0.05440.17790.0319-0.03710.04130.50810.0705-0.53010.02460.19630.0267-0.02610.18340.00280.19-26.564-0.919-10.5179
21.2129-0.8651-1.49241.08431.51562.49980.0869-0.02920.0918-0.0486-0.0148-0.0273-0.17260.0253-0.09350.17860.0113-0.02570.11360.01770.1479-18.3826-0.5445-8.4328
32.86560.45080.04893.597-0.19762.57050.00820.067-0.3776-0.06250.0624-0.04580.1229-0.0193-0.05790.0960.0138-0.00440.12360.00970.1412-8.4924-22.8331-27.9558
41.3756-0.3197-0.10962.92780.25842.029-0.0588-0.1099-0.0424-0.00970.0147-0.0325-0.0093-0.01690.04820.09890.0016-0.02180.10930.00240.0934-16.1997-14.07428.2021
52.1920.5241-1.96261.6012-1.28522.48490.0615-0.09830.06390.0996-0.089-0.0168-0.0430.4512-0.00320.1383-0.0135-0.01660.190.01370.13314.7095-24.433-19.0261
62.44820.9002-2.79381.3753-1.71733.9821-0.0957-0.1511-0.08480.1047-0.1094-0.15620.07610.44170.23160.1438-0.0073-0.02490.23610.02440.14485.7776-25.6964-19.2772
71.8389-2.816-1.10749.76921.19217.405-0.1927-0.7465-0.98280.7110.30650.5680.6531-0.4685-0.15090.40020.01470.04590.40820.03840.384-30.5446-0.930611.9778
88.46970.45742.68556.4792-0.69970.98330.311-0.55680.20440.4364-0.02850.2284-0.10.0755-0.29810.42490.06820.03920.4918-0.02740.3068-29.68944.757412.4457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:31)
2X-RAY DIFFRACTION2(chain H and resid 32:124)
3X-RAY DIFFRACTION3(chain H and resid 125:214)
4X-RAY DIFFRACTION4(chain L and resid 1:105)
5X-RAY DIFFRACTION5(chain L and resid 106:160)
6X-RAY DIFFRACTION6(chain L and resid 161:213)
7X-RAY DIFFRACTION7(chain P and resid 305:312)
8X-RAY DIFFRACTION8(chain P and resid 313:318)

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