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- PDB-5hm1: Llama VHH 2E7 in complex with gp41 -

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Basic information

Entry
Database: PDB / ID: 5hm1
TitleLlama VHH 2E7 in complex with gp41
Components
  • gp41
  • lama VHH antibody 2E7
KeywordsIMMUNE SYSTEM / HIV / gp41 / gp120 / antibodies
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 / 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 / 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
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 speciesLama glama (llama)
HIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.962 Å
AuthorsHock, M. / Caillat, C. / Haffke, M. / Weissenhorn, W.
CitationJournal: To Be Published
Title: Structure of HIV neutralizing VHH 2E7 in complex with gp41 peptide
Authors: Strokappe, N.M. / Hock, M. / Rutten, L. / McCoy, L.E. / Back, J.W. / Caillat, C. / Haffke, M. / Weiss, R.A. / Chen, L. / Kwong, P. / Weissenhorn, W. / Verrips, T.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
A: lama VHH antibody 2E7
D: gp41
B: lama VHH antibody 2E7
E: gp41
C: lama VHH antibody 2E7
F: gp41


Theoretical massNumber of molelcules
Total (without water)43,9276
Polymers43,9276
Non-polymers00
Water0
1
A: lama VHH antibody 2E7
D: gp41


Theoretical massNumber of molelcules
Total (without water)14,6422
Polymers14,6422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-13 kcal/mol
Surface area6990 Å2
MethodPISA
2
B: lama VHH antibody 2E7
E: gp41


Theoretical massNumber of molelcules
Total (without water)14,6422
Polymers14,6422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-13 kcal/mol
Surface area6950 Å2
MethodPISA
3
C: lama VHH antibody 2E7
F: gp41


Theoretical massNumber of molelcules
Total (without water)14,6422
Polymers14,6422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-13 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.950, 121.260, 132.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody lama VHH antibody 2E7


Mass: 12808.206 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide gp41 / / Envelope glycoprotein gp160 / Env polyprotein


Mass: 1834.123 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_HXB2R (virus) / References: UniProt: P04578

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes pH 7.0 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.95→44.6874 Å / Num. obs: 12538 / % possible obs: 96.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.6
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.9 / % possible all: 34.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B50

4b50


Resolution: 2.962→44.6874 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 604 4.83 %Random selection
Rwork0.1942 ---
obs0.1967 12504 93.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.962→44.6874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 0 0 3087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063153
X-RAY DIFFRACTIONf_angle_d1.2564272
X-RAY DIFFRACTIONf_dihedral_angle_d14.0811128
X-RAY DIFFRACTIONf_chiral_restr0.05456
X-RAY DIFFRACTIONf_plane_restr0.005555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9617-3.25960.38161360.29312361X-RAY DIFFRACTION77
3.2596-3.73110.28281510.23343109X-RAY DIFFRACTION99
3.7311-4.70.23521510.16823157X-RAY DIFFRACTION99
4.7-44.68740.20041660.16773273X-RAY DIFFRACTION98
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)
12.26161.83544.22872.49444.53359.087-1.06660.42191.5882-0.646-0.18690.3264-1.3730.68311.2710.74440.0773-0.14850.44340.04670.81332.196640.4527159.0869
22.6645-0.71350.19833.6844-1.38961.82870.2542-0.093-0.38510.17990.45980.410.22370.3091-0.02770.31980.2617-0.17890.5148-0.28770.726817.356822.945155.221
35.77520.02070.96963.67431.84011.44510.09550.9183-0.2163-0.45780.2598-0.6442-0.44990.6439-0.38770.56530.03860.06580.5638-0.06040.350434.636533.1376161.9362
47.2638-0.54461.21952.8601-0.59960.58690.23220.10020.3883-0.07450.09570.8795-0.7157-0.4341-0.08320.26340.12870.04840.5138-0.03430.415717.637335.9347167.2611
57.6916-0.61791.59521.2575-0.34472.4842-0.4967-1.1462-0.54580.56470.317-0.01320.3472-0.41070.1180.4524-0.0501-0.02430.4264-0.13770.385824.58527.6029173.842
63.64870.9632-3.22254.0858-1.83954.7785-0.071-0.6216-0.2937-0.22090.0347-0.45350.30531.22940.18210.38430.104-0.03650.5344-0.08080.497335.217127.5134166.2147
71.20420.52830.33273.63320.82242.94690.2789-0.0848-0.46130.42-0.10020.0886-0.01520.307-0.01320.42460.0668-0.0520.3011-0.17510.522521.269224.9058163.4214
81.5057-0.77260.97012.14590.77334.24810.06120.2531-0.4434-0.49690.20840.1726-1.12660.6107-0.05050.4727-0.14240.10940.1173-0.39160.320130.585839.8971166.7682
94.10343.57894.70655.91342.37737.1893-0.8970.03620.8476-0.8855-0.2190.0187-0.57220.41390.51610.41130.02650.04260.4755-0.04770.366233.145145.3379166.9137
105.14573.931-4.07953.1333-3.19833.2802-0.6883-0.4060.1748-0.99150.37160.404-0.11490.38920.34390.2820.0514-0.29260.6227-0.08140.60616.348529.5844156.5303
112.55222.01292.51673.29311.55983.15521.09540.51470.40810.465-0.59440.1540.57810.2775-0.32550.47220.05250.1060.4462-0.110.398333.126137.9145179.6461
121.32521.5726-0.05842.31940.10180.0687-1.07260.97130.2837-0.92530.71010.2551-0.88520.76050.19550.6684-0.0066-0.03860.53020.01870.72539.15038.0471142.0033
132.2330.85490.52212.4911-0.85074.56350.4331-0.16620.24330.5654-0.15770.40010.13160.8017-0.26940.4630.0931-0.03860.4615-0.13760.560119.513114.0271154.4395
144.6448-3.34271.8692.4314-1.28330.81740.0602-0.18730.0617-0.12260.28560.7081-0.2364-0.2514-0.2680.71650.9856-0.20820.40410.17730.79221.31425.8585146.9822
153.4001-0.2422-2.08153.6848-0.92082.15870.35141.2489-0.2848-0.58970.4752-0.63410.65560.5556-0.21840.36860.16910.07810.6114-0.11610.415623.06490.7147148.7539
166.21612.0174-1.69153.98581.28122.23970.2641-1.1241-0.99770.5377-0.1164-0.14110.41720.6309-0.01740.54160.2054-0.1280.5155-0.07110.392816.1564-0.8693159.7304
170.313-1.4171-0.0216.9294-1.18173.84440.17420.03240.72220.5520.13661.6078-0.6938-1.2778-0.3970.49770.20470.04380.94410.03060.7936.41576.6128157.378
182.64042.1667-0.29782.68641.15892.05890.0883-0.28880.5914-0.0006-0.00750.18330.22660.2638-0.09490.49350.1872-0.05820.3258-0.05680.448615.55285.1372151.8137
193.45794.37681.6815.59881.21612.6672-0.70130.3537-0.2136-1.1520.6179-0.06990.06180.35660.18590.52860.1056-0.03270.3765-0.02410.427813.29533.3503144.0072
202.23212.2122-0.28092.86790.68982.59070.3754-0.2569-0.14580.1412-0.14550.3268-0.1111-0.4567-0.0960.58280.15520.03790.37610.13370.48776.0474-9.1694153.2425
219.12281.63473.43182.86621.26876.4644-0.3979-0.19370.23310.47660.28590.3144-0.395-0.06850.37380.44580.0802-0.06490.438-0.04940.41359.40128.6221138.7755
224.41341.5623-5.40484.1414-2.19666.6461-0.48660.840.458-0.63180.3219-0.8978-0.33670.2738-0.14620.2082-0.44590.18080.8502-0.09440.57520.714426.0029129.7969
233.80220.49013.01893.1018-0.06192.5891-0.03440.3211-1.1041-0.37310.6361-0.63430.55960.5844-0.30940.4068-0.0276-0.00460.4564-0.09150.422316.140814.9145134.6409
247.47471.925-0.70687.46230.19358.25390.32740.60360.52310.64750.22431.4982-0.2969-1.5122-0.74220.46940.00570.1150.56180.06650.77315.516419.2246140.3328
258.00022.49821.8095.0775-1.51675.03760.39-0.43790.1152-0.03690.4489-0.2788-0.16940.5699-0.5470.41110.106-0.0020.628-0.18060.298419.549922.7683141.8836
267.53460.94164.20161.42461.33253.8618-0.43010.45290.6755-0.05670.17780.1073-0.67480.68210.27010.5234-0.1297-0.08950.4138-0.00750.42039.146128.136129.446
278.76081.7451.37144.20981.4684.20530.92230.55570.51980.5155-0.14140.09230.412-0.0329-0.55810.5725-0.05740.00710.36630.06030.28596.094214.0614124.2042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 17 through 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 45 )
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 66 )
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 76 )
7X-RAY DIFFRACTION7chain 'A' and (resid 77 through 90 )
8X-RAY DIFFRACTION8chain 'A' and (resid 91 through 102 )
9X-RAY DIFFRACTION9chain 'A' and (resid 103 through 112 )
10X-RAY DIFFRACTION11chain 'D' and (resid 582 through 596 )
11X-RAY DIFFRACTION12chain 'B' and (resid 1 through 7 )
12X-RAY DIFFRACTION13chain 'B' and (resid 8 through 24 )
13X-RAY DIFFRACTION14chain 'B' and (resid 25 through 33 )
14X-RAY DIFFRACTION15chain 'B' and (resid 34 through 45 )
15X-RAY DIFFRACTION16chain 'B' and (resid 46 through 66 )
16X-RAY DIFFRACTION17chain 'B' and (resid 67 through 76 )
17X-RAY DIFFRACTION18chain 'B' and (resid 77 through 102 )
18X-RAY DIFFRACTION19chain 'B' and (resid 103 through 112 )
19X-RAY DIFFRACTION20chain 'E' and (resid 582 through 596 )
20X-RAY DIFFRACTION21chain 'C' and (resid 1 through 33 )
21X-RAY DIFFRACTION22chain 'C' and (resid 34 through 45 )
22X-RAY DIFFRACTION23chain 'C' and (resid 46 through 66 )
23X-RAY DIFFRACTION24chain 'C' and (resid 67 through 76 )
24X-RAY DIFFRACTION25chain 'C' and (resid 77 through 90 )
25X-RAY DIFFRACTION26chain 'C' and (resid 91 through 112 )
26X-RAY DIFFRACTION27chain 'F' and (resid 582 through 596 )

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