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- PDB-7b4t: Broadly neutralizing DARPin bnD.1 in complex with the HIV-1 envel... -

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Basic information

Entry
Database: PDB / ID: 7b4t
TitleBroadly neutralizing DARPin bnD.1 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
Components
  • Broadly neutralizing DARPin bnD.1
  • HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
KeywordsDE NOVO PROTEIN / HIV / V3 / conformation / neutralization / DARPins / antibodies
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFriedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. ...Friedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. / Morin, M. / Eroglu, M. / Liechti, T. / Ivan, B. / Reinberg, T. / Schaefer, J. / Karakus, U. / Ursprung, S. / Mann, A. / Rusert, P. / Kouyos, R.D. / Robinson, J.A. / Gunthard, H.F. / Pluckthun, A. / Trkola, A.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_192689 Switzerland
Swiss National Science Foundation310030B_166676 Switzerland
Swiss National Science Foundation31003A_146278 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization.
Authors: Friedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. / Morin, M. / Eroglu, M. / Liechti, T. / Ivan, B. / ...Authors: Friedrich, N. / Stiegeler, E. / Glogl, M. / Lemmin, T. / Hansen, S. / Kadelka, C. / Wu, Y. / Ernst, P. / Maliqi, L. / Foulkes, C. / Morin, M. / Eroglu, M. / Liechti, T. / Ivan, B. / Reinberg, T. / Schaefer, J.V. / Karakus, U. / Ursprung, S. / Mann, A. / Rusert, P. / Kouyos, R.D. / Robinson, J.A. / Gunthard, H.F. / Pluckthun, A. / Trkola, A.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
A: Broadly neutralizing DARPin bnD.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4706
Polymers19,0852
Non-polymers3844
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-60 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.980, 67.050, 95.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)


Mass: 1603.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Broadly neutralizing DARPin bnD.1


Mass: 17481.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 0.2 M Ammonium sulphate, 12% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.95→38.925 Å / Num. obs: 30369 / % possible obs: 98.7 % / Redundancy: 4.49 % / Biso Wilson estimate: 25.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.17 / Χ2: 0.959 / Net I/σ(I): 8.27 / Num. measured all: 136355 / Scaling rejects: 275
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-24.271.4981.079671230322650.5521.71298.3
2-2.064.291.211.389184217821410.551.38198.3
2.06-2.124.3030.9891.739272219521550.7171.12998.2
2.12-2.184.3720.8841.898901207120360.7421.00698.3
2.18-2.254.3360.7112.498885207620490.7870.80998.7
2.25-2.334.3860.6782.538369193919080.8650.76898.4
2.33-2.424.4910.5053.588506191118940.8890.57199.1
2.42-2.524.5850.4054.338061178817580.9240.45698.3
2.52-2.634.6880.2995.898199176117490.9570.33699.3
2.63-2.764.5770.2776.267556166616510.9570.31399.1
2.76-2.914.5140.2047.997168160215880.9760.2399.1
2.91-3.084.3660.1679.096575151815060.9770.1999.2
3.08-3.33.9040.1211.015434140413920.9830.13999.1
3.3-3.564.2860.0815.795482130112790.9940.09198.3
3.56-3.94.6910.06620.445549121111830.9960.07497.7
3.9-4.365.1180.0525.565589110610920.9980.05698.7
4.36-5.045.1190.04827.1148739579520.9980.05499.5
5.04-6.175.2040.05524.0641748078020.9980.06199.4
6.17-8.725.170.03932.9432886386360.9990.04399.7
8.72-38.9254.8620.0339.9816193383330.9990.03398.5

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.95→38.925 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 815 4.98 %
Rwork0.2094 15566 -
obs0.2115 16381 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.98 Å2 / Biso mean: 38.9064 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: final / Resolution: 1.95→38.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 20 85 1431
Biso mean--82.01 34.15 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041384
X-RAY DIFFRACTIONf_angle_d0.6361879
X-RAY DIFFRACTIONf_chiral_restr0.04208
X-RAY DIFFRACTIONf_plane_restr0.004250
X-RAY DIFFRACTIONf_dihedral_angle_d16.71814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9501-2.07230.36751340.2998251498
2.0723-2.23230.29381400.2594253198
2.2323-2.45690.29851270.2322258099
2.4569-2.81230.25651240.2086260599
2.8123-3.54290.24711490.212258699
3.5429-38.9250.21131410.1752275099
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)
15.43721.6907-2.96357.79583.17776.0338-0.2497-0.4351-0.29660.89660.3991-1.54570.51051.85880.14430.3125-0.0034-0.08510.56-0.06550.50030.2102-9.473420.0411
21.97790.4537-0.29214.0587-0.60962.2761-0.07170.2557-0.28750.06450.1550.05720.13230.0626-0.12320.215-0.00950.01510.3577-0.00110.2696-6.5539-17.4959-3.7698
36.49774.84692.07943.98262.40679.5608-0.0802-0.16130.2265-0.56890.0238-0.0174-0.56310.2628-0.02850.3128-0.04450.00010.30480.02970.3311-8.4877-9.0487-9.6082
43.6923-0.97652.86332.3169-0.5942.45250.09420.0594-0.3532-0.02660.0310.28420.16940.0014-0.06960.236-0.01350.04330.2773-0.01270.2732-10.7126-16.9781.7213
56.07631.81560.84144.24731.47973.4151-0.2164-0.10720.3015-0.15480.1176-0.0638-0.3131-0.01810.07260.1891-0.00160.02470.1767-0.00650.2258-9.4921-5.20171.0909
60.89070.3105-0.49431.2621-0.6782.3443-0.0078-0.220.1010.0814-0.0586-0.09730.04090.04330.05360.2270.0234-0.00930.3035-0.02380.2691-10.2534-8.995911.0766
72.80722.3425-0.4755.90783.30673.6268-0.03630.43690.7405-0.5914-0.18040.0626-0.9891-1.09490.22980.34410.0521-0.05410.2665-0.02160.3059-14.8352.23026.4672
80.6379-0.9387-0.36464.2623-0.71295.66060.0967-0.1670.07030.2631-0.1499-0.2311-0.11330.09620.05360.2476-0.00220.03340.3329-0.05980.2524-10.5907-3.59519.7015
92.33080.9552-0.4655.18621.2566.73950.07790.14731.5492-0.2308-0.04350.3537-1.5667-0.26280.04790.47720.06060.03180.322-0.07550.4042-13.25737.574416.2226
102.09071.18620.33895.9144-1.98456.8415-0.0996-0.7514-0.09860.636-0.2356-0.03810.4822-0.43830.33330.4149-0.02320.07360.4319-0.1030.2794-12.8002-4.029628.2782
111.58121.6906-0.55812.3543-2.60977.24010.4687-0.0971-0.67430.9751-0.6303-0.5613-0.48840.90730.20940.4083-0.1013-0.0550.3725-0.05230.3881-4.5813.080628.6645
122.2224-1.475-1.68846.83711.91158.3109-0.12730.27830.7750.2146-0.04220.4679-1.8367-0.26250.14940.7590.00630.01260.3572-0.01960.3372-11.595610.4828.2139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 15 )B1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 24 )A9 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 35 )A25 - 35
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 49 )A36 - 49
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 68 )A50 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 92 )A69 - 92
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 102 )A93 - 102
8X-RAY DIFFRACTION8chain 'A' and (resid 103 through 125 )A103 - 125
9X-RAY DIFFRACTION9chain 'A' and (resid 126 through 135 )A126 - 135
10X-RAY DIFFRACTION10chain 'A' and (resid 136 through 148 )A136 - 148
11X-RAY DIFFRACTION11chain 'A' and (resid 149 through 158 )A149 - 158
12X-RAY DIFFRACTION12chain 'A' and (resid 159 through 170 )A159 - 170

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