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- PDB-6mnr: Rhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide -

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Basic information

Entry
Database: PDB / ID: 6mnr
TitleRhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide
Components
  • Ab DH753 heavy chain Fab fragment
  • Ab DH753 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: 2.201 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 DH753 heavy chain Fab fragment
L: Ab DH753 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5777
Polymers49,2273
Non-polymers3504
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-69 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.855, 71.817, 134.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules P

#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

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Antibody , 2 types, 2 molecules HL

#2: Antibody Ab DH753 heavy chain Fab fragment


Mass: 24036.021 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 DH753 light chain


Mass: 22795.984 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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Non-polymers , 3 types, 88 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium sulfate decahydrate, 20% PEG 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23370 / % possible obs: 100 % / Redundancy: 7.9 % / Rpim(I) all: 0.035 / Rsym value: 0.073 / Net I/σ(I): 27.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1154 / Rpim(I) all: 0.237 / Rsym value: 0.525 / % possible all: 99.9

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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: PDBs 5JR1, 5IIE

5jr1

5iie


Resolution: 2.201→43.41 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 1999 8.57 %Random selection
Rwork0.1919 ---
obs0.1972 23313 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.201→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 19 84 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093417
X-RAY DIFFRACTIONf_angle_d1.1294647
X-RAY DIFFRACTIONf_dihedral_angle_d14.2781198
X-RAY DIFFRACTIONf_chiral_restr0.04530
X-RAY DIFFRACTIONf_plane_restr0.005588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2008-2.25580.31761390.25191485X-RAY DIFFRACTION99
2.2558-2.31680.34391420.23861517X-RAY DIFFRACTION100
2.3168-2.38490.39021390.24651478X-RAY DIFFRACTION100
2.3849-2.46190.31441400.22931493X-RAY DIFFRACTION100
2.4619-2.54990.3451420.22071506X-RAY DIFFRACTION100
2.5499-2.6520.27421400.22011498X-RAY DIFFRACTION100
2.652-2.77270.27091410.22961503X-RAY DIFFRACTION100
2.7727-2.91880.30481410.221504X-RAY DIFFRACTION100
2.9188-3.10160.30021430.22671517X-RAY DIFFRACTION100
3.1016-3.3410.23131430.22671522X-RAY DIFFRACTION100
3.341-3.67710.27751430.19141524X-RAY DIFFRACTION100
3.6771-4.20880.21981450.161558X-RAY DIFFRACTION100
4.2088-5.30110.17471470.13451555X-RAY DIFFRACTION100
5.3011-43.41880.23321540.17431654X-RAY DIFFRACTION100
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)
12.3089-0.053-1.08963.6996-0.03495.2986-0.20430.4156-0.1878-0.34440.1949-0.01460.39020.17030.03650.3255-0.0452-0.05970.31080.07430.2799-29.2767-10.9584-17.2738
26.2040.4940.33143.1894-0.5463.09680.0369-0.3866-0.1422-0.0517-0.01480.02830.13630.18470.00080.1821-0.0252-0.01170.26970.05750.1987-24.9575-9.1973-8.9719
33.22741.9157-1.65923.3203-2.67224.65470.05310.1120.1355-0.54470.0055-0.10260.05150.0567-0.0130.38370.01060.02780.1620.01270.3397-42.07242.5331-33.7422
44.2504-1.97491.26725.374-1.72386.1834-0.0464-0.80750.62660.7581-0.1044-0.1659-1.0892-0.2430.11820.6604-0.1069-0.01890.534-0.24930.477-23.333413.55680.3671
54.1875-1.13241.52276.4639-1.3685.060.0918-0.39830.80730.307-0.2259-0.0811-0.45160.00640.16780.2775-0.0926-0.01360.3441-0.08640.3701-20.67539.909-6.3074
64.94130.46952.76014.74781.45534.4530.1344-0.1019-0.2457-0.09680.09230.2513-0.1945-0.3122-0.19850.42860.03980.05430.19650.03920.3598-51.33614.9447-28.4847
75.64042.20143.61984.82422.94622.9161-0.33750.31310.6860.9596-0.1909-0.52670.15191.13450.53070.399-0.0196-0.0470.50670.07780.3964-10.5215-4.51872.2845
88.48593.94681.33733.76453.59684.7988-0.5395-0.63020.4260.41390.221-1.0744-0.16510.61160.12430.2393-0.0427-0.16320.59980.06020.5259-11.1933-4.5522-2.1874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:26)
2X-RAY DIFFRACTION2(chain H and resid 27:113)
3X-RAY DIFFRACTION3(chain H and resid 114:214)
4X-RAY DIFFRACTION4(chain L and resid 2:32)
5X-RAY DIFFRACTION5(chain L and resid 33:106A)
6X-RAY DIFFRACTION6(chain L and resid 107:208)
7X-RAY DIFFRACTION7(chain P and resid 305:309)
8X-RAY DIFFRACTION8(chain P and resid 312:320)

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