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

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Basic information

Entry
Database: PDB / ID: 6snd
Titlecrystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide
Components
  • Envelope glycoprotein gp160
  • LN01 heavy chain
  • LN01 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 / virus-mediated perturbation of host defense response ...: / 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 / virus-mediated perturbation of host defense response / 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 / 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 / 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 / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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: LN01 light chain
B: LN01 heavy chain
C: Envelope glycoprotein gp160
L: LN01 light chain
H: LN01 heavy chain
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,52011
Polymers104,0876
Non-polymers1,4335
Water0
1
A: LN01 light chain
B: LN01 heavy chain
C: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6165
Polymers52,0433
Non-polymers5732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31 kcal/mol
Surface area21780 Å2
MethodPISA
2
L: LN01 light chain
H: LN01 heavy chain
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9046
Polymers52,0433
Non-polymers8613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-30 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.707, 137.707, 146.719
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'P671 - 689
221chain 'C'C671 - 689
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
173chain 'L'L1 - 212
183chain 'L'L300
293chain 'A'A1 - 212
2103chain 'A'A300

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules ALBH

#1: Antibody LN01 light chain


Mass: 23230.734 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 LN01 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 CP

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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, 3 molecules

#5: 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
#6: Chemical ChemComp-PC / PHOSPHOCHOLINE / Phosphocholine


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PSF / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLSERINE / Phosphatidylserine


Mass: 455.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34NO10P / 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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7,5 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→48.91 Å / Num. obs: 26213 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 76.56 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.09 / Rrim(I) all: 0.186 / Net I/σ(I): 8.8
Reflection shellResolution: 3.1→3.31 Å / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4662 / CC1/2: 0.671

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.17 Å / SU ML: 0.4803 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.3254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2668 1336 5.11 %
Rwork0.2383 24796 -
obs0.2397 26132 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.3 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 92 0 7210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317404
X-RAY DIFFRACTIONf_angle_d0.837310109
X-RAY DIFFRACTIONf_chiral_restr0.05021135
X-RAY DIFFRACTIONf_plane_restr0.00631259
X-RAY DIFFRACTIONf_dihedral_angle_d15.75022603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.210.44671240.40472441X-RAY DIFFRACTION99.88
3.21-3.340.37771280.33932433X-RAY DIFFRACTION99.49
3.34-3.490.31150.29622459X-RAY DIFFRACTION99.92
3.49-3.680.32181210.28942461X-RAY DIFFRACTION100
3.68-3.910.3231250.29442452X-RAY DIFFRACTION99.96
3.91-4.210.29241510.24282453X-RAY DIFFRACTION99.5
4.21-4.630.20111830.19592415X-RAY DIFFRACTION99.92
4.63-5.30.22471150.1882524X-RAY DIFFRACTION99.62
5.3-6.670.24361330.20532511X-RAY DIFFRACTION99.62
6.67-47.170.23571410.20282647X-RAY DIFFRACTION98.9
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)
10.0216417978262-0.02846476604890.0271594747477-0.0277724502592-0.1163875068760.0491496009422-0.4521351008750.2745588876530.1212575306790.536509074192-0.6852317425090.38278492202-0.6174158023160.1225760379921.41410711408E-70.5083502878930.050942387398-0.09624385621690.996497637934-0.1572277114730.0998059891810.9072489715-12.1238645127-28.414677999
20.0334010921472-0.03723105160640.0696292241404-0.001643885827240.04448347306680.0401206536984-0.2154501462650.1876038497050.4497569581920.496061922183-0.401600561859-0.0779090644078-0.1762712825220.321609549744.9691700629E-80.9033864200090.1033623942240.02977187283580.445557418863-0.1300231075220.370851182511-2.45478256342-9.2915845444328.142336637
30.8139828309080.121333529403-0.359469547211.27020185194-0.4696926086960.327028165748-0.0176864222067-0.0965349954528-0.00868922355689-0.175259413094-0.0301684137726-0.15189662745-0.00380165319434-0.1322395542813.49283410515E-100.438448201370.00464154819390.06696835869160.4137256091910.03672928993090.32923691070330.9777062124-13.2467948954-16.0233985519
40.976877464885-0.542632840756-0.196908669590.6764522012370.4521055848761.24076632470.0858063012210.0466105286409-0.0171510428470.0687634964346-0.004666413295690.122306619275-0.0126806265514-0.05050114151261.55171121033E-90.3202646165880.0594855516396-0.01075365020870.344470736950.07028238967990.3417100603053.15611503456-24.01884422810.6078820152
51.53246140546-0.3829802801660.7119998122490.156945842715-0.04996475115271.04611010115-0.0501628222525-0.1546516147310.147611120030.00734417907645-0.0967172640196-0.3767994834390.150051741667-0.0710514391957-3.43162478107E-100.386257617788-0.0175284158854-0.05120399839130.4120012018130.1150510634360.74646477455456.1122268775-16.07685095938.10850999678
60.45073377767-1.00129952436-0.1373375744911.579958738070.8742893318151.05431104289-0.07107792055120.163791910704-0.171878962217-0.0408489740881-0.068498871206-0.0326176881618-0.201774840872-0.0577664883618-7.32423183137E-100.4781759003520.1000264614130.01814361137260.467311096238-0.0289765467040.48185937290617.5324997378-47.7361850799-11.6656127593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain P
2X-RAY DIFFRACTION2chain C
3X-RAY DIFFRACTION3(chain H and resseq 2:114) or (chain L and resseq 1:106)
4X-RAY DIFFRACTION4(chain B and resseq 2:114) or (chain A and resseq 1:106)
5X-RAY DIFFRACTION5(chain H and resseq 115:215) or (chain L and resseq 107:213)
6X-RAY DIFFRACTION6(chain B and resseq 115:215) or (chain A and resseq 107:213)

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