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- PDB-7b4v: Broadly neutralizing DARPin bnD.2 in complex with the HIV-1 envel... -

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Basic information

Entry
Database: PDB / ID: 7b4v
TitleBroadly neutralizing DARPin bnD.2 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
Components
  • Broadly neutralizing DARPin bnD.2
  • 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 / molecular replacement / Resolution: 1.4 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
C: Broadly neutralizing DARPin bnD.2
A: Broadly neutralizing DARPin bnD.2
B: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
D: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,97113
Polymers30,6974
Non-polymers2749
Water6,936385
1
C: Broadly neutralizing DARPin bnD.2
D: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4686
Polymers15,3482
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-40 kcal/mol
Surface area6670 Å2
MethodPISA
2
A: Broadly neutralizing DARPin bnD.2
B: HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5037
Polymers15,3482
Non-polymers1555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-45 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.630, 69.340, 69.920
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 Broadly neutralizing DARPin bnD.2


Mass: 13744.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)


Mass: 1603.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→49.235 Å / Num. obs: 49189 / % possible obs: 100 % / Redundancy: 12.751 % / Biso Wilson estimate: 14.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.17 / Χ2: 1.061 / Net I/σ(I): 9.77 / Num. measured all: 627203 / Scaling rejects: 382
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
1.4-1.4412.692.1861.3945493358635850.4472.278100
1.44-1.4813.5281.7251.8547336349934990.6381.793100
1.48-1.5213.4791.4062.2746097342034200.6991.461100
1.52-1.5713.4161.1272.7944234329732970.8121.172100
1.57-1.6213.290.9743.2442500319831980.8441.013100
1.62-1.6713.1620.8243.8440947311131110.880.857100
1.67-1.7412.8270.6434.7538623301130110.9080.669100
1.74-1.8111.9280.4995.7934532289528950.9420.522100
1.81-1.8912.1760.3857.3833910278527850.9640.402100
1.89-1.9812.6720.2949.4333670265726570.9770.306100
1.98-2.0913.4410.23112.1634153254125410.9870.24100
2.09-2.2113.1590.18614.0631712241024100.990.194100
2.21-2.3712.7960.16215.4228932226122610.9920.169100
2.37-2.5612.4680.13817.0426458212221220.9940.144100
2.56-2.812.1650.11619.4123879196319630.9950.121100
2.8-3.1311.1430.09621.2619756177317730.9950.101100
3.13-3.6110.2950.07823.9516513160516040.9970.08399.9
3.61-4.4312.3060.06631.9316589134813480.9980.069100
4.43-6.2613.1250.06133.814136107710770.9990.064100
6.26-49.23512.2360.0537.277336326320.9990.052100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

Resolution: 1.4→49.235 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 2471 5.02 %
Rwork0.1646 46716 -
obs0.1662 49187 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.67 Å2 / Biso mean: 22.9998 Å2 / Biso min: 9.81 Å2
Refinement stepCycle: final / Resolution: 1.4→49.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 9 385 2493
Biso mean--20.33 30.99 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042272
X-RAY DIFFRACTIONf_angle_d0.6753111
X-RAY DIFFRACTIONf_chiral_restr0.054364
X-RAY DIFFRACTIONf_plane_restr0.004418
X-RAY DIFFRACTIONf_dihedral_angle_d18.958820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.42690.37661170.31092582
1.4269-1.4560.31121380.28672547
1.456-1.48770.25011220.27072570
1.4877-1.52230.31321540.24942549
1.5223-1.56040.27691350.22782550
1.5604-1.60250.26111260.21792577
1.6025-1.64970.23031310.20362573
1.6497-1.7030.22431340.20152577
1.703-1.76380.23331340.19552578
1.7638-1.83440.22321490.18732566
1.8344-1.91790.18281360.1732582
1.9179-2.01910.17341210.15462608
2.0191-2.14560.18351200.14742597
2.1456-2.31120.2021540.14762605
2.3112-2.54380.17911410.14462604
2.5438-2.91180.18581490.14442627
2.9118-3.66840.15551620.1432631
3.6684-49.2350.17291480.13712793
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)
12.976-3.4863-3.9577.17482.63588.21930.00890.5291-0.1239-0.3949-0.07390.517-0.0469-0.59710.07910.16210.0014-0.00170.17210.05970.2317-15.69010.3705-5.9916
26.5621-1.4336-2.81650.40920.23183.39250.1225-0.47931.2630.7120.00030.8284-0.11980.0606-0.04240.28530.01190.11820.1714-0.0380.5234-13.91267.20030.9967
31.1497-0.1467-0.4482.43221.59482.93540.06380.19170.23730.0402-0.06660.22110.0284-0.1455-0.00370.13370.01210.01970.11530.03140.1444-13.2562-4.7793-1.4339
47.2531-0.9179-2.04665.5188-1.49247.02320.1742-0.16070.69020.2790.0962-0.0523-0.47850.0721-0.27780.1838-0.00330.06240.1183-0.0280.2-10.70521.0668.4968
51.43250.4455-0.08620.83230.46020.86110.0262-0.04690.1064-0.003-0.01840.0381-0.0180.0192-0.00190.12810.00660.01880.11810.0070.1027-7.0173-11.72551.7974
67.1502-1.799-3.88786.4223-2.49737.93810.0334-0.55330.50440.1871-0.09220.0876-0.27960.41830.11450.1649-0.01770.02210.1734-0.04370.1419-1.6264-5.635911.3196
71.7220.60170.08671.13790.49071.47670.0345-0.1553-0.05030.1341-0.02560.01830.1068-0.0161-0.01680.12560.01680.01020.11410.01460.0977-1.1338-17.88053.8032
83.06181.6568-4.35495.5692-2.24866.86440.0599-1.1874-0.0350.6855-0.0318-0.35120.20560.58830.01050.22290.0122-0.01540.317-0.00030.17056.109-14.529311.7495
98.39511.75452.21217.21850.14815.8535-0.2097-0.39160.21480.35260.0876-0.37240.24350.31860.11420.16020.0632-0.00370.23540.04110.198212.06380.3134-3.7773
101.9344-0.07810.2111.6214-0.09121.75770.009-0.0535-0.06690.0387-0.0741-0.108-0.00610.15520.06210.1172-0.0116-0.00840.15170.0360.11715.66459.0589-11.3095
116.97834.8136-1.63218.0438-0.62685.19550.1507-0.71550.1550.6414-0.26770.1027-0.31940.20420.09510.2095-0.0046-0.04070.16340.01250.1247-0.884517.8033-4.4051
121.5989-0.6314-0.15281.6527-0.82151.80680.02050.0128-0.09710.0124-0.0168-0.0072-0.1059-0.040700.1155-0.0161-0.01060.1190.00660.0854-4.362216.5285-18.8131
135.66555.8824-6.26816.322-6.54477.0180.3874-0.08190.53950.61-0.18750.2751-0.5358-0.1309-0.2270.27160.01520.01720.195-0.00770.1948-7.91124.7578-11.2278
145.41896.6882-5.89998.89-7.32296.43340.05530.28060.0966-0.19130.2710.54770.0058-0.4133-0.32740.14710.0005-0.02680.19090.02540.161-9.32325.0089-17.9133
152.76783.3441-3.1135.5544-5.22417.61760.13510.00830.2167-0.07610.00450.28050.2082-0.1119-0.13610.15170.0077-0.01650.14770.02280.1076-2.99920.8976-17.6227
168.47494.6856-1.69135.9249-1.13281.93990.2598-0.2271-0.11890.1668-0.3303-0.4010.02970.20920.09020.15680.01970.0060.15360.00480.10953.0045-11.8046-7.5834
174.81510.0449-2.71885.1976-3.1414.55820.11690.22980.0824-0.2062-0.02660.2285-0.0977-0.1989-0.08490.11770.0075-0.0060.10770.0020.0741-4.4815-9.1214-9.4505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 13 through 23 )C13 - 23
2X-RAY DIFFRACTION2chain 'C' and (resid 24 through 35 )C24 - 35
3X-RAY DIFFRACTION3chain 'C' and (resid 36 through 60 )C36 - 60
4X-RAY DIFFRACTION4chain 'C' and (resid 61 through 70 )C61 - 70
5X-RAY DIFFRACTION5chain 'C' and (resid 71 through 93 )C71 - 93
6X-RAY DIFFRACTION6chain 'C' and (resid 94 through 102 )C94 - 102
7X-RAY DIFFRACTION7chain 'C' and (resid 103 through 126 )C103 - 126
8X-RAY DIFFRACTION8chain 'C' and (resid 127 through 138 )C127 - 138
9X-RAY DIFFRACTION9chain 'A' and (resid 13 through 36 )A13 - 36
10X-RAY DIFFRACTION10chain 'A' and (resid 37 through 93 )A37 - 93
11X-RAY DIFFRACTION11chain 'A' and (resid 94 through 102 )A94 - 102
12X-RAY DIFFRACTION12chain 'A' and (resid 103 through 126 )A103 - 126
13X-RAY DIFFRACTION13chain 'A' and (resid 127 through 140 )A127 - 140
14X-RAY DIFFRACTION14chain 'B' and (resid 1 through 6 )B1 - 6
15X-RAY DIFFRACTION15chain 'B' and (resid 7 through 15 )B7 - 15
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 6 )D1 - 6
17X-RAY DIFFRACTION17chain 'D' and (resid 7 through 15 )D7 - 15

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