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- PDB-6snc: crystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide -

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Basic information

Entry
Database: PDB / ID: 6snc
Titlecrystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide
Components
  • Envelope glycoprotein gp160
  • LNO1 Heavy Chain
  • LNO1 Light Chain
KeywordsIMMUNE SYSTEM / gp41 / antibody / complex / MPER
Function / homology
Function and homology information


: / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane ...: / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane / plasma membrane
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
dodecyl 2-(trimethylammonio)ethyl phosphate / PHOSPHOCHOLINE / PHOSPHATE ION / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCaillat, C. / Pinto, D. / Corti, D. / Fenwick, C. / Pantaleo, G. / Weissenhorn, W.
Funding support Switzerland, France, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1114725 Switzerland
Bill & Melinda Gates FoundationOPP1032144 Switzerland
European CommissionNo. 681137, H2020 EAVI France
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01.
Authors: Pinto, D. / Fenwick, C. / Caillat, C. / Silacci, C. / Guseva, S. / Dehez, F. / Chipot, C. / Barbieri, S. / Minola, A. / Jarrossay, D. / Tomaras, G.D. / Shen, X. / Riva, A. / Tarkowski, M. / ...Authors: Pinto, D. / Fenwick, C. / Caillat, C. / Silacci, C. / Guseva, S. / Dehez, F. / Chipot, C. / Barbieri, S. / Minola, A. / Jarrossay, D. / Tomaras, G.D. / Shen, X. / Riva, A. / Tarkowski, M. / Schwartz, O. / Bruel, T. / Dufloo, J. / Seaman, M.S. / Montefiori, D.C. / Lanzavecchia, A. / Corti, D. / Pantaleo, G. / Weissenhorn, W.
History
DepositionAug 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LNO1 Light Chain
B: LNO1 Heavy Chain
L: LNO1 Light Chain
H: LNO1 Heavy Chain
P: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,64513
Polymers104,2936
Non-polymers1,3527
Water00
1
A: LNO1 Light Chain
B: LNO1 Heavy Chain
C: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7427
Polymers52,1463
Non-polymers5954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: LNO1 Light Chain
H: LNO1 Heavy Chain
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9036
Polymers52,1463
Non-polymers7573
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.762, 136.762, 146.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'P'P1 - 210
221chain 'C'C1 - 210
132(chain 'H' and (resid 2 through 126 or resid 135 through 215))H2 - 126
142(chain 'H' and (resid 2 through 126 or resid 135 through 215))H135 - 215
252(chain 'B' and (resid 2 through 126 or resid 135 through 215))B2 - 126
262(chain 'B' and (resid 2 through 126 or resid 135 through 215))B135 - 215
173(chain 'A' and (resid 1 through 210 or resid 300))A671 - 689
283chain 'L'L671 - 689

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules ALBH

#1: Antibody LNO1 Light Chain


Mass: 23333.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody LNO1 Heavy Chain


Mass: 25520.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein/peptide / Sugars , 2 types, 4 molecules PC

#3: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 3292.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: G3DH64, UniProt: P04578*PLUS
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 3 types, 5 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H38NO4P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P / Feature type: SUBJECT OF INVESTIGATION

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Details

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: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Hepes pH 7.5 11 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2018
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.2→47 Å / Num. obs: 23542 / % possible obs: 99.69 % / Redundancy: 9.6 % / Biso Wilson estimate: 84.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2291 / CC1/2: 0.688 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→47 Å / SU ML: 0.482 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8211 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2538 1208 5.13 %
Rwork0.2128 22319 -
obs0.2149 23527 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.3 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7090 0 83 0 7173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01047375
X-RAY DIFFRACTIONf_angle_d1.304710084
X-RAY DIFFRACTIONf_chiral_restr0.07281129
X-RAY DIFFRACTIONf_plane_restr0.0081250
X-RAY DIFFRACTIONf_dihedral_angle_d25.0532546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.330.39331270.33122426X-RAY DIFFRACTION99.49
3.33-3.480.30671120.27822446X-RAY DIFFRACTION99.8
3.48-3.660.33231210.27742449X-RAY DIFFRACTION99.84
3.66-3.890.34041240.24882446X-RAY DIFFRACTION99.57
3.89-4.190.2731560.22812450X-RAY DIFFRACTION99.81
4.19-4.610.2341790.19182409X-RAY DIFFRACTION99.88
4.61-5.280.20931120.17132524X-RAY DIFFRACTION100
5.28-6.650.25361350.20092522X-RAY DIFFRACTION100
6.65-47.010.21331420.19722647X-RAY DIFFRACTION99.29
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)
18.269268016882.008798048760.8074091423063.84818887932-1.350312631193.59892351754-0.1770971918580.597240640714-0.0265851444821-0.699691742402-0.00604503502043-0.1696964584750.0946534269052-0.005356734704520.1736662967170.7664565861080.03806346585050.1214681037610.603293362690.03360608704330.50932572330636.0667358179-13.3643042918-23.5804830074
25.236025265422.565811819043.365496657082.22128080753-0.6521804769047.706529956760.3947712340791.11777410311.148604140941.40134876291-0.6824562719770.922155218722-1.06103564217-1.066594979750.2807530353371.023163006330.257753811126-0.06168711798291.22095125246-0.1996400012611.1210206868310.0451152662-11.0231299124-28.5868180364
34.28237306007-0.163551230876-0.003684026255614.91482636681-1.449727483260.4282529513310.374248144086-0.4759693763080.5509291331260.472291333993-0.644205913359-0.136007847924-1.21004866865-0.1750850941070.2010414484621.442621897240.005453582018110.1209380775221.1307861509-0.3670034319781.04118212202-3.20038570494-8.1466365686128.4115173394
47.64963591092-0.854740315541-1.236616931654.00991735970.3683010080616.256065261330.118312595926-0.6758620196130.05907704257420.5332443675770.219073587505-0.02719831190870.353532318990.140460070145-0.3252210799040.6365352059040.0363026498362-0.04201264754230.6632812235930.0004800913822770.5198937851111.2675552154-27.009938518818.150855536
53.74099163216-1.347561017890.1967957398236.065620420980.5747747681998.425904522390.4543620715490.1179262400230.064658979893-0.397317120312-0.2540582264230.552877289287-0.306390607674-0.785613169673-0.2895729354030.5221109930790.0964867147575-0.02796662824590.5714687114170.05149953107450.704141795692-4.4969891916-20.48302269165.00963451938
64.25637571531-0.0249605445885-0.4003001275411.773141804540.8994210648826.254568911140.119329994288-0.0494133841980.2893923272690.0790552504441-0.08548328550680.0715439790981-0.311346999675-0.230523339098-0.004588408178650.7563467065640.04514274920460.05284281013440.742288300669-0.03431641304240.80111915760923.1540776044-11.962275787-6.51387432773
75.89380419069-0.3152772204441.122523449781.712408183841.01035973265.715067164130.09149076046390.267821633895-0.6090180698180.00706728185134-0.227039705546-0.7439356042770.5502332589940.6831806134160.1334215384820.6606759581190.008523030351560.01158072961630.6941498071920.1833739584911.1661967789756.5921692292-21.1813222170.48608047716
85.81778890035-1.176243683330.7761451837053.348975985410.5682839629085.67594436147-0.236176476629-0.8856064296980.6352077745810.5409006498240.0247904416391-0.876869546127-0.6081096797540.4472604513480.1608646916120.732626089773-0.0674209385814-0.1373759203470.7921375291340.06789476916150.89065695980154.577593225-11.680707830214.018879426
93.78284883872-0.841749592495-0.03425838225054.645346229221.712244411284.815897170160.08984366050150.293502867550.278365304191-0.7664966326820.000454595948582-0.602459769799-0.6693094240530.0879253821786-0.1852542380370.9767799128640.1514249746010.09428181530210.765398712539-0.03250891937990.96866168114824.5898635636-47.0312487292-11.1437601326
105.29118137873-1.37496995479-1.830811854744.609047837751.548942360585.53996970560.273377085361.01031074128-0.526839670949-0.677342249539-0.6557869700970.755996355776-0.450190840494-0.8119082230230.3690071263650.7614626886490.236257731295-0.1243324204010.720810524547-0.1391490223930.7594654236718.78702142063-47.6056239028-11.7041748064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'H' and resid 2 through 115)
2X-RAY DIFFRACTION2(chain 'P' and resid 671 through 689)
3X-RAY DIFFRACTION3(chain 'C' and resid 671 through 689)
4X-RAY DIFFRACTION4(chain 'A' and resid 1 through 107)
5X-RAY DIFFRACTION5(chain 'B' and resid 2 through 115)
6X-RAY DIFFRACTION6(chain 'L' and resid 1 through 107)
7X-RAY DIFFRACTION7(chain 'H' and resid 116 through 215)
8X-RAY DIFFRACTION8(chain 'L' and resid 108 through 300)
9X-RAY DIFFRACTION9(chain 'A' and resid 108 through 300)
10X-RAY DIFFRACTION10(chain 'B' and resid 116 through 216)

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