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- PDB-7aej: Crystal structure of asymmetric HIV-1 gp41 containing all membran... -

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Basic information

Entry
Database: PDB / ID: 7aej
TitleCrystal structure of asymmetric HIV-1 gp41 containing all membrane anchors
Components
  • 2H10
  • Envelope glycoprotein gp160,Envelope glycoprotein gp160
KeywordsVIRAL PROTEIN / membrane fusion
Function / homology
Function and homology information


: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / virion membrane / structural molecule activity / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsCaillat, C. / Guilligay, D. / Weissenhorn, W.
CitationJournal: Elife / Year: 2021
Title: Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies.
Authors: Caillat, C. / Guilligay, D. / Torralba, J. / Friedrich, N. / Nieva, J.L. / Trkola, A. / Chipot, C.J. / Dehez, F.L. / Weissenhorn, W.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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Assembly

Deposited unit
C: Envelope glycoprotein gp160,Envelope glycoprotein gp160
A: Envelope glycoprotein gp160,Envelope glycoprotein gp160
B: Envelope glycoprotein gp160,Envelope glycoprotein gp160
D: 2H10


Theoretical massNumber of molelcules
Total (without water)78,8274
Polymers78,8274
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-141 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.750, 101.414, 234.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Envelope glycoprotein gp160,Envelope glycoprotein gp160 / Env polyprotein


Mass: 21824.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and ...Details: Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: B2CPZ5
#2: Antibody 2H10


Mass: 13351.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VHH / Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium citrate pH 6.0 0.2M ammonium sulfate 20 % PEG 200 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.8→49.56 Å / Num. obs: 11179 / % possible obs: 78.01 % / Redundancy: 9.1 % / Biso Wilson estimate: 85.33 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.23 / Net I/σ(I): 4.75
Reflection shellResolution: 3.8→3.936 Å / Num. unique obs: 631 / CC1/2: 0.628

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1env, 4b50

1env

4b50


Resolution: 3.8→49.56 Å / SU ML: 0.5169 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3077 550 5.99 %
Rwork0.2653 8634 -
obs0.2677 9184 78.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.76 Å2
Refinement stepCycle: LAST / Resolution: 3.8→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 0 0 4440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344517
X-RAY DIFFRACTIONf_angle_d0.65986114
X-RAY DIFFRACTIONf_chiral_restr0.0455694
X-RAY DIFFRACTIONf_plane_restr0.004765
X-RAY DIFFRACTIONf_dihedral_angle_d13.5135584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.180.34331090.28691624X-RAY DIFFRACTION60.22
4.18-4.790.29821170.24522064X-RAY DIFFRACTION75.44
4.79-6.030.30411550.29192311X-RAY DIFFRACTION84.63
6.03-49.560.30261690.2562635X-RAY DIFFRACTION92.12
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)
11.12837911302-1.50318139749-0.9621022913633.639045388250.1049526859594.206747691560.2768553358921.16566756689-0.2591760888040.170683848228-0.153793861821-0.6509280292930.3161217529121.40721249122-1.798954322670.20565024438-0.41076826658-0.89605225293-0.106816459198-0.552804192584-0.431161303132-10.8891235352-8.65318627233-55.3547395399
22.82200546099-0.813370900688-0.7896903652313.089238917881.563897414221.4381907930.409377253118-0.481048364068-0.695208250722-0.14113477822-0.312833438037-0.03078262345561.3644841654-1.7959385917-0.1564697577080.390929512171-0.1023559692890.06697924923630.8249986361250.0636365397050.46271759942-7.55677508261-17.0738416626-53.3999065768
30.0841235144001-0.0332746356914-0.1244124638110.04081959942740.08751938661360.154729216252-0.06562401351170.0138220111696-0.757294196049-0.913589771851-0.2892888253610.2682945899680.317264086520.09722374363381.087517127E-61.615236857650.115392179101-0.280940766021.63547042065-0.03711877563631.40774286263-32.4916757251-23.3802565037-100.930487982
41.36396185528-1.46605565932-0.1046022838273.731867618110.7551089260912.114315379140.256552570555-1.079718132790.3967412595980.953683106360.1562839923830.04844881235360.412432366041-0.8931870269420.3108765612860.613678329338-0.156562824164-0.3438450788820.530442906592-0.06458547118680.844335038679-13.6663131624-4.42005757432-46.2511294024
50.566000360483-0.379064147936-0.6291269503230.8328840181210.6677774064180.859805253531-0.2222708519760.3183122455311.572837351780.5663946733-0.489345095461-0.1123210762680.1438570950840.355736794558-0.01066230413960.616720922219-0.0658140647158-0.07748500444070.539723112664-0.01357038753030.546866728797-5.977989953091.39206829945-52.1166030251
62.80899450762-0.365176643918-0.5429512128722.994819983642.898716390616.790155976140.436266691849-0.5545232780110.0172103555249-0.1815824004561.262392183380.1764691246191.13266412245-1.207470900192.835873350311.69188658896-0.22992377398-1.297320835970.9924501435560.1607676416070.424664164182-43.8687826578-6.74459937902-80.7081434136
71.124431919950.730620731384-0.08482953958192.11557802785-1.264438355460.6986400198650.649987570914-0.439163601187-0.281558490555-0.006430982016140.08838732408390.3590966171280.590114713804-0.3834450349340.2974121463060.4675799516930.2636008360740.1654946557840.866426382418-0.4083342312270.378512191067-15.1321588093-12.3846410064-52.2222232653
80.527178977151-0.432722774491-0.1287327560261.95982847325-1.212954749761.05568766607-0.0784617794991-0.4672957106310.239284555969-0.189712053538-0.9157264823310.5598622118550.571391622549-1.75768407616-0.0009925235737570.5211177271660.00187156077681-0.03269729043381.2190625654-0.2052628503991.04515487516-29.9534281911-15.6981023411-66.071084681
93.34787029139-1.0737890555-1.691722373622.64526440035-0.3903722440491.474990166510.3036522500970.3623449929330.0878762778713-0.312844222197-0.00303614991470.05909813023890.189871331084-0.2191403815595.47689005994E-60.512105152369-0.0107866928019-0.1674659203720.42541761335-0.04994444917570.928117953987-32.165911590517.816235583-63.3357168162
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 518 through 588 )CA518 - 5881 - 71
22chain 'C' and (resid 589 through 670 )CA589 - 67072 - 120
33chain 'C' and (resid 671 through 706 )CA671 - 706121 - 156
44chain 'A' and (resid 527 through 588 )AB527 - 5881 - 62
55chain 'A' and (resid 589 through 663 )AB589 - 66363 - 99
66chain 'A' and (resid 664 through 693 )AB664 - 693100 - 129
77chain 'B' and (resid 518 through 627 )BC518 - 6271 - 72
88chain 'B' and (resid 628 through 700 )BC628 - 70073 - 145
99chain 'D' and (resid 1 through 112 )DD1 - 1121 - 121

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