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- PDB-7dng: DARPin 63_B7 in complex with linear V3-crown (MN) peptide -

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Basic information

Entry
Database: PDB / ID: 7dng
TitleDARPin 63_B7 in complex with linear V3-crown (MN) peptide
Components
  • DARPin 63_B7
  • linear V3-crown (MN) peptide
KeywordsDE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / anti-HIV
Biological speciessynthetic construct (others)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsWu, Y. / Plueckthun, 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 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DARPin 63_B7
B: linear V3-crown (MN) peptide


Theoretical massNumber of molelcules
Total (without water)20,0052
Polymers20,0052
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-4 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.530, 94.530, 39.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

21A-356-

HOH

31A-363-

HOH

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Components

#1: Protein DARPin 63_B7


Mass: 18384.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue
#2: Protein/peptide linear V3-crown (MN) peptide


Mass: 1620.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% Jeffamine ED-2001, 0.1M HEPES pH 7.0

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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: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→40.93 Å / Num. obs: 38156 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 1 / Rmerge(I) obs: 0.1055 / Rrim(I) all: 0.1101 / Net I/σ(I): 13.72
Reflection shellResolution: 1.42→1.471 Å / Redundancy: 11.9 % / Rmerge(I) obs: 6.44 / Num. unique obs: 3784 / CC1/2: 0.117 / R split: 0.36 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx


Resolution: 1.42→40.93 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1907 5 %
Rwork0.1776 --
obs0.1789 38139 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 0 187 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041439
X-RAY DIFFRACTIONf_angle_d0.6121975
X-RAY DIFFRACTIONf_dihedral_angle_d12.201535
X-RAY DIFFRACTIONf_chiral_restr0.052230
X-RAY DIFFRACTIONf_plane_restr0.004262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.45550.42811360.40942583X-RAY DIFFRACTION100
1.4555-1.49490.3971330.37272540X-RAY DIFFRACTION100
1.4949-1.53890.36531350.36422557X-RAY DIFFRACTION100
1.5389-1.58850.32491350.33172579X-RAY DIFFRACTION100
1.5885-1.64530.30881360.30742585X-RAY DIFFRACTION100
1.6453-1.71120.30411360.26922583X-RAY DIFFRACTION100
1.7112-1.78910.28511350.2422562X-RAY DIFFRACTION100
1.7891-1.88340.2511360.2152571X-RAY DIFFRACTION100
1.8834-2.00140.22581360.20222588X-RAY DIFFRACTION100
2.0014-2.15590.19811360.17122581X-RAY DIFFRACTION100
2.1559-2.37290.17581370.15582601X-RAY DIFFRACTION100
2.3729-2.71620.19511360.15162597X-RAY DIFFRACTION100
2.7162-3.42180.16291380.15882622X-RAY DIFFRACTION100
3.4218-40.930.18331420.14342683X-RAY DIFFRACTION100
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)
13.10313.42511.21958.07050.91212.1257-0.11081.2428-0.0761-0.80970.4196-0.9827-0.21220.9178-0.2220.43390.00310.00390.4785-0.05760.344448.4777-14.617-5.0554
22.3211.2340.77062.93680.80651.4979-0.024-0.06860.27080.2376-0.08120.3026-0.0837-0.15890.12410.23270.02490.02030.2054-0.01330.196934.3476-18.7168-4.8759
35.2477-0.17890.41215.00390.11693.2890.0211-0.75830.45660.9661-0.25930.9061-0.0928-0.71270.10960.3511-0.06630.18870.464-0.1560.514718.1967-25.385-1.9125
44.4324-0.9522-0.81346.65024.0977.7369-0.11040.53970.2885-0.6844-0.01541.109-0.1201-0.37530.05950.2307-0.0335-0.10930.34690.06160.425619.4161-26.6008-16.4882
56.161-4.4806-2.55554.9535-0.73698.33260.2227-0.66010.89660.46240.08811.5191-0.0374-1.1041-0.15090.222-0.12170.06010.5087-0.09110.582114.5424-35.1388-8.8362
67.91625.4379-4.95766.3438-2.20083.66160.0891-0.5048-0.2680.3641-0.3081-0.29680.07010.12150.23720.24-0.0143-0.02150.30530.00610.186635.7604-34.3547-10.0238
75.9783-1.1314-4.64568.1261-0.35768.6767-0.3977-0.2233-0.31470.41830.1216-0.4520.30670.59760.32270.25370.0291-00.2960.03070.182242.4619-27.7395-9.7127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 148 )
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 169 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 12 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 18 )

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