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

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Basic information

Entry
Database: PDB / ID: 6mns
TitleRhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide
Components
  • Ab DH753 heavy chain Fab fragment
  • Ab DH753 light chain
  • Envelope glylcoprotein
KeywordsIMMUNE SYSTEM / HIV-1 gp120 V3 antibody
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / identical protein binding
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Envelope glylcoprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Apr 3, 2024Group: 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 glylcoprotein
H: Ab DH753 heavy chain Fab fragment
L: Ab DH753 light chain
Q: Envelope glylcoprotein
A: Ab DH753 heavy chain Fab fragment
B: Ab DH753 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2768
Polymers99,0866
Non-polymers1902
Water27015
1
P: Envelope glylcoprotein
H: Ab DH753 heavy chain Fab fragment
L: Ab DH753 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6384
Polymers49,5433
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-37 kcal/mol
Surface area20530 Å2
MethodPISA
2
Q: Envelope glylcoprotein
A: Ab DH753 heavy chain Fab fragment
B: Ab DH753 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6384
Polymers49,5433
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-37 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.920, 138.315, 71.678
Angle α, β, γ (deg.)90.00, 91.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Envelope glylcoprotein


Mass: 2711.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A9Q0A0, UniProt: P05877*PLUS
#2: Antibody Ab DH753 heavy chain Fab fragment


Mass: 24036.021 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) / Variant (production host): HEK-293
#3: Antibody Ab DH753 light chain


Mass: 22795.984 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) / Variant (production host): HEK-293
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium dihydrogen phosphate, 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-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / 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: 2.7→50 Å / Num. obs: 25304 / % possible obs: 99.5 % / Redundancy: 4 % / Rpim(I) all: 0.055 / Rsym value: 0.081 / Net I/σ(I): 17.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1299 / Rpim(I) all: 0.278 / Rsym value: 0.473 / % possible all: 100

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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: Previously solved DH753 structure (also in submission)

Resolution: 2.7→38.772 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1978 7.92 %Random selection
Rwork0.1699 ---
obs0.1769 24977 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6678 0 10 15 6703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096847
X-RAY DIFFRACTIONf_angle_d1.2459310
X-RAY DIFFRACTIONf_dihedral_angle_d15.0932410
X-RAY DIFFRACTIONf_chiral_restr0.0451065
X-RAY DIFFRACTIONf_plane_restr0.0061181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.76760.34441450.23651671X-RAY DIFFRACTION100
2.7676-2.84240.36861340.23591619X-RAY DIFFRACTION100
2.8424-2.9260.31451500.2191655X-RAY DIFFRACTION100
2.926-3.02040.3311400.22941625X-RAY DIFFRACTION100
3.0204-3.12830.32341410.22471665X-RAY DIFFRACTION100
3.1283-3.25350.31591450.21121629X-RAY DIFFRACTION100
3.2535-3.40150.28441450.20231649X-RAY DIFFRACTION100
3.4015-3.58070.32521360.19361643X-RAY DIFFRACTION100
3.5807-3.80490.32311340.19021636X-RAY DIFFRACTION99
3.8049-4.09840.24081470.15531619X-RAY DIFFRACTION100
4.0984-4.51020.22471390.13491649X-RAY DIFFRACTION99
4.5102-5.16160.19811430.11721653X-RAY DIFFRACTION99
5.1616-6.49810.20761370.1551652X-RAY DIFFRACTION100
6.4981-38.77590.21381420.16181634X-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)
16.90240.802-1.20843.8628-1.24283.1566-0.1818-0.3068-0.0410.3890.0477-0.4866-0.12070.18280.10250.48790.02530.00170.4399-0.14070.462531.2218-9.716845.272
22.8925-0.6666-0.61235.87742.06845.69380.0430.0073-0.25320.22780.00290.07910.82330.1612-0.03470.51870.00440.03940.50710.02850.36813.9588-34.306634.8545
34.00431.04411.34093.9279-1.46068.1337-0.27530.41530.1072-0.71310.3228-0.442-0.49080.2216-0.13360.5106-0.08710.17420.5159-0.05210.557132.7216-3.801924.0424
46.82120.6727-2.75675.26360.52147.72050.17250.1927-0.4762-0.2713-0.17420.2959-0.1516-0.3834-0.04620.49040.0218-0.11270.35240.00940.43034.7556-28.517223.0147
58.3015-0.4212.27263.2271-0.94333.2157-0.25550.2264-0.1593-0.29670.0951-0.2341-0.08510.09790.16640.44450.001-0.02230.3618-0.06590.429110.086511.1339-9.5021
63.62020.24720.76136.61382.97425.7416-0.0382-0.10430.1143-0.06170.08140.0998-0.5642-0.0225-0.01590.36820.0431-0.05010.37250.01330.3289-7.783135.40570.8784
75.8462-1.7039-0.11924.6075-0.87168.4965-0.2884-0.4556-0.27660.67420.3218-0.0228-0.0222-0.1885-0.03070.38310.0649-0.05480.4250.04250.391811.87495.320711.2435
85.528-2.74671.65485.9884-1.05668.0407-0.1942-0.0450.28270.5758-0.10590.25490.5215-0.19920.25770.4398-0.05240.05880.3733-0.0740.3675-17.016729.893612.8751
98.3751-3.25380.03086.9207-2.12595.52340.0790.9921-1.0365-0.7577-0.4405-1.1540.52330.76920.23830.50770.16230.06530.5351-0.04620.845724.84410.8259-2.1659
107.39414.95732.46863.76080.07296.44140.1402-0.17680.0952-0.22010.6693-1.3514-1.43091.3345-0.66810.52-0.1030.0690.9305-0.25881.171445.11570.771938.0834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:113)
2X-RAY DIFFRACTION2(chain A and resid 114:214)
3X-RAY DIFFRACTION3(chain B and resid 2:108)
4X-RAY DIFFRACTION4(chain B and resid 109:208)
5X-RAY DIFFRACTION5(chain H and resid 1:111)
6X-RAY DIFFRACTION6(chain H and resid 112:213)
7X-RAY DIFFRACTION7(chain L and resid 2:106)
8X-RAY DIFFRACTION8(chain L and resid 107:208)
9X-RAY DIFFRACTION9(chain P and resid 306:321)
10X-RAY DIFFRACTION10(chain Q and resid 305:319)

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