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- PDB-7dnf: DARPin 63_B7 in complex with V3-IY (MN) crown mimetic -

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Basic information

Entry
Database: PDB / ID: 7dnf
TitleDARPin 63_B7 in complex with V3-IY (MN) crown mimetic
Components
  • DARPin 63_B7
  • V3-IY (MN) crown mimetic 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: 1.78 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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
A: DARPin 63_B7
B: V3-IY (MN) crown mimetic peptide
C: DARPin 63_B7
D: DARPin 63_B7
E: V3-IY (MN) crown mimetic peptide
F: DARPin 63_B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,13114
Polymers77,3636
Non-polymers7698
Water11,512639
1
A: DARPin 63_B7
B: V3-IY (MN) crown mimetic peptide
C: DARPin 63_B7
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The DARPin 63_B7 is supposed to bind one V3-IY (MN) crown mimetic. However, only two V3-IY (MN) crown mimetics with 4 DARPin 63_B7 are found in asymmetric unit. The details ...Evidence: gel filtration, The DARPin 63_B7 is supposed to bind one V3-IY (MN) crown mimetic. However, only two V3-IY (MN) crown mimetics with 4 DARPin 63_B7 are found in asymmetric unit. The details will be explained in the publication.
  • 39 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)38,9696
Polymers38,6813
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-62 kcal/mol
Surface area14560 Å2
MethodPISA
2
D: DARPin 63_B7
E: V3-IY (MN) crown mimetic peptide
F: DARPin 63_B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1628
Polymers38,6813
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-59 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.350, 105.980, 64.020
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DARPin 63_B7


Mass: 18384.520 Da / Num. of mol.: 4
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 V3-IY (MN) crown mimetic peptide


Mass: 1912.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% w/v PEG 3350, 0.2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→48.26 Å / Num. obs: 59433 / % possible obs: 96.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1276 / Rrim(I) all: 0.07273 / Net I/σ(I): 7.67
Reflection shellResolution: 1.78→1.844 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.572 / Num. unique obs: 5571 / CC1/2: 0.271 / % possible all: 90.79

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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: 1.78→48.26 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 1486 2.5 %
Rwork0.1871 --
obs0.188 59419 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4993 0 40 639 5672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045152
X-RAY DIFFRACTIONf_angle_d0.5487009
X-RAY DIFFRACTIONf_dihedral_angle_d9.6213025
X-RAY DIFFRACTIONf_chiral_restr0.039805
X-RAY DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7801-1.83760.34131260.30564939X-RAY DIFFRACTION91
1.8376-1.90330.34561290.29525000X-RAY DIFFRACTION92
1.9033-1.97950.31891290.26935052X-RAY DIFFRACTION93
1.9795-2.06960.27731320.23385142X-RAY DIFFRACTION94
2.0696-2.17870.27721340.21545243X-RAY DIFFRACTION97
2.1787-2.31520.22281390.2015408X-RAY DIFFRACTION99
2.3152-2.49390.25451370.18615353X-RAY DIFFRACTION99
2.4939-2.74490.22511390.18275423X-RAY DIFFRACTION100
2.7449-3.1420.20471390.18265416X-RAY DIFFRACTION99
3.142-3.95830.17821400.1555464X-RAY DIFFRACTION99
3.9583-48.260.20851420.16515493X-RAY DIFFRACTION99
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)
14.42960.36152.92042.48991.96343.1290.27130.2912-0.4861-0.62560.17370.81330.3133-0.0531-0.30160.40410.0073-0.08370.282-0.06420.48577.22-32.77285.1731
25.9264-0.9813-3.44546.054-0.55522.2125-0.02410.0922-0.6081-0.4392-0.1326-0.30380.435-0.02650.0620.3235-0.0331-0.00430.2936-0.07130.309317.1012-35.14038.5104
37.262-2.1316-3.72562.99351.37472.36220.26140.66450.1003-0.1807-0.0414-0.0268-0.0597-0.1819-0.02960.2430.0021-0.01920.2875-0.01170.2236.2878-23.997910.1231
44.5748-1.5746-1.39313.4651.59881.8419-0.00290.0208-0.03410.02910.0543-0.15290.05340.0548-0.13610.2224-0.01920.00370.21630.00440.184112.9412-24.048219.0349
54.66151.7079-3.08312.9768-1.42413.60440.1036-0.45190.10620.1806-0.1258-1.0629-0.29770.96840.02620.23220.0078-0.01030.30670.02530.254521.5458-21.610423.9751
67.3615-5.07213.82417.8485-1.34045.7283-0.08-0.268-0.12880.31710.07330.28080.1103-0.1602-0.02580.2663-0.00140.01020.1683-0.03320.15629.3357-16.173229.8064
78.54662.1803-4.55562.0337-1.25292.497-0.0829-0.7011-0.11930.40370.0001-0.49560.29810.910.19320.32520.0396-0.09440.3331-0.01920.245520.3108-18.235134.2262
87.3663-2.5819-3.79873.95360.43194.59420.1162-0.270.91780.39590.1770.1833-0.4339-0.4072-0.27930.3761-0.02220.01030.2979-0.0560.23198.8499-9.624134.0867
93.5153-4.33111.87886.694-3.93737.763-0.4613-1.08730.28841.41480.1975-0.3717-0.16110.29140.40290.65-0.0310.01080.5448-0.05870.225312.1909-16.091144.0982
103.1318-2.8011.72483.5948-2.88586.1418-0.1255-1.2577-0.84431.37790.4795-0.43130.5573-0.7833-0.31580.5207-0.0477-0.0330.45830.09240.43851.8032-28.377729.2925
114.11462.90780.76522.66052.53429.2781-0.01160.0317-0.2879-0.15360.0063-0.08950.3439-0.00120.0660.25310.03020.00380.22430.02210.29611.9819-30.734422.9691
129.65422.0571-4.7838.2707-3.11968.2667-0.2709-0.3587-0.03820.22450.3060.02480.02270.0499-0.10060.257-0.0114-0.02530.30430.07830.2137-12.5641-34.730228.614
132.42590.3417-1.23142.8753-0.43423.4774-0.0309-0.10030.07420.12070.1428-0.0737-0.04390.0567-0.04630.2340.00850.00130.22570.01350.2321-10.9708-27.781321.8089
149.1481-2.4829-3.04691.3965-0.21257.157-0.30540.295-0.65950.11020.11580.56720.9556-0.75850.14450.3432-0.07470.02060.3102-0.00260.3612-16.7189-37.984617.7823
152.02140.1732-1.13851.8001-0.38883.9128-0.1291-0.0288-0.1694-0.07280.181-0.0491-0.06880.0107-0.08860.20460.0107-0.00070.2701-0.00490.2224-11.5-26.200113.062
162.1397-1.2009-2.01541.3765-0.70467.6793-0.410.3242-0.9843-0.18820.04340.13030.82690.13960.17790.3427-0.02850.04650.2729-0.04190.3515-14.7643-35.83347.1127
172.13830.0159-1.05922.9794-0.61964.2846-0.0253-0.01160.17720.00230.0744-0.3082-0.09160.1293-0.00130.2165-0.0056-0.02960.271-0.0220.2566-9.378-23.33513.9287
182.0395-1.6734-1.31384.8416-0.08228.0374-0.0808-0.0664-0.9142-0.33160.15150.20850.7957-0.14590.12240.2774-0.00090.01840.2299-0.03290.2523-11.1524-33.4214-2.656
195.93411.1663-1.57844.0154-0.62693.5907-0.02390.509-0.1207-0.5472-0.0461-0.3765-0.0967-0.00540.03320.2858-0.00080.00130.3032-0.01030.2388-6.342-23.3882-7.3848
207.1685-1.94834.24636.1682-3.4473.52490.1619-0.69150.76080.57890.04781.0356-0.5467-0.3989-0.11940.3169-0.01680.08710.2778-0.09580.42737.64348.236723.2841
217.3075-1.66180.76745.1394-4.53064.8895-0.0117-0.21820.95870.7599-0.1212-0.7929-1.05990.170.13480.43870.0024-0.00570.2656-0.1040.356116.852510.864824.8154
223.1190.62081.48392.30080.1122.35420.10730.06140.02140.0351-0.0624-0.02930.01980.0215-0.03710.17060.01260.01730.1561-0.0050.155312.2802-0.311316.5629
233.0657-0.51574.90622.2353-0.44087.9255-0.03740.24480.10680.3640.1009-0.7240.3071.0273-0.08940.24920.0572-0.02040.32470.00390.252123.0253-2.690210.2562
246.30514.4703-2.96118.2019-0.16458.56830.04690.35640.0211-0.215-0.06390.2869-0.2082-0.25220.00750.28220.05660.01360.2258-0.02340.184211.4695-8.12423.2429
257.96591.8741-0.94841.8837-0.75622.4518-0.01090.41610.0767-0.95870.3172-0.9142-0.24961.1766-0.06440.45220.10370.08260.4639-0.06730.268922.732-5.7578-0.2731
268.93324.24114.77085.04554.02935.71290.20510.4253-1.0193-0.15210.3137-0.1810.53090.3783-0.4110.4210.0703-0.01570.2838-0.01770.212511.4749-14.5229-1.2449
275.876-0.7913-2.58046.32382.88496.45240.19261.15280.4115-1.2559-0.2544-0.1628-0.52221.05450.09580.55130.0424-0.01720.7011-0.0040.174615.1939-7.3764-10.8285
285.19482.8546-1.77397.8103-4.44993.7442-0.15881.37970.0604-0.6610.2276-0.2689-0.16670.2297-0.38570.3752-0.05070.00550.52510.08850.25794.24914.8542.6146
296.80331.52940.72292.8299-3.52695.7780.17310.07790.4599-0.0705-0.2186-0.051-0.68060.3512-0.05790.3236-0.01950.03440.20750.01240.22293.37866.25429.3706
303.8144-1.03754.93935.7791-1.29937.8902-0.07940.65810.538-0.38360.043-0.23-0.36670.34440.05860.2216-0.0345-0.0120.28920.07430.1942-10.027510.48352.3223
311.7015-0.2346-0.13222.6881-0.68553.7768-0.03310.0942-0.0766-0.14540.1641-0.22010.14230.12430.01910.2269-0.02070.00930.23470.00570.2249-9.65513.24879.2045
327.88161.33733.40223.90960.29319.01570.21230.22570.6221-0.1732-0.22960.4417-0.6983-0.5307-0.02240.26040.0401-0.01130.31090.01470.3044-15.969413.389911.5714
332.2744-0.97090.03972.9218-0.12175.06-0.03790.0733-0.05480.05470.0886-0.0770.1170.13510.02670.2379-0.00320.020.24350.01450.2617-10.54721.095518.6676
342.03721.00051.05734.4887-1.36487.18450.07-0.32710.90640.14120.05890.6566-0.9943-0.2606-0.03630.36740.02380.02780.273-0.02240.3125-15.572311.635522.8879
351.52011.22830.6363.4539-1.85356.4081-0.42470.0415-0.32740.23310.16850.00810.3817-0.28160.01520.308-0.02990.04120.2877-0.0290.2812-13.3248-4.175525.0176
368.7697-1.25242.59489.0888-1.54985.9926-0.328-0.09610.3870.79390.2151-0.272-0.3410.20670.22950.34240.0147-0.00640.2394-0.00390.223-9.09835.298931.7835
374.302-0.54232.07324.1458-0.08812.7564-0.2843-0.51410.13491.03590.2788-0.3950.0276-0.06610.03140.50140.06910.01910.3431-0.02960.277-8.7151-1.169738.4257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 125 )
7X-RAY DIFFRACTION7chain 'A' and (resid 126 through 134 )
8X-RAY DIFFRACTION8chain 'A' and (resid 135 through 148 )
9X-RAY DIFFRACTION9chain 'A' and (resid 149 through 166 )
10X-RAY DIFFRACTION10chain 'B' and (resid 5 through 12 )
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 20 )
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 35 )
13X-RAY DIFFRACTION13chain 'C' and (resid 36 through 59 )
14X-RAY DIFFRACTION14chain 'C' and (resid 60 through 68 )
15X-RAY DIFFRACTION15chain 'C' and (resid 69 through 92 )
16X-RAY DIFFRACTION16chain 'C' and (resid 93 through 101 )
17X-RAY DIFFRACTION17chain 'C' and (resid 102 through 125 )
18X-RAY DIFFRACTION18chain 'C' and (resid 126 through 134 )
19X-RAY DIFFRACTION19chain 'C' and (resid 135 through 168 )
20X-RAY DIFFRACTION20chain 'D' and (resid 13 through 24 )
21X-RAY DIFFRACTION21chain 'D' and (resid 25 through 35 )
22X-RAY DIFFRACTION22chain 'D' and (resid 36 through 92 )
23X-RAY DIFFRACTION23chain 'D' and (resid 93 through 102 )
24X-RAY DIFFRACTION24chain 'D' and (resid 103 through 125 )
25X-RAY DIFFRACTION25chain 'D' and (resid 126 through 134 )
26X-RAY DIFFRACTION26chain 'D' and (resid 135 through 148 )
27X-RAY DIFFRACTION27chain 'D' and (resid 149 through 165 )
28X-RAY DIFFRACTION28chain 'E' and (resid 5 through 12 )
29X-RAY DIFFRACTION29chain 'E' and (resid 13 through 20 )
30X-RAY DIFFRACTION30chain 'F' and (resid 13 through 35 )
31X-RAY DIFFRACTION31chain 'F' and (resid 36 through 59 )
32X-RAY DIFFRACTION32chain 'F' and (resid 60 through 69 )
33X-RAY DIFFRACTION33chain 'F' and (resid 70 through 92 )
34X-RAY DIFFRACTION34chain 'F' and (resid 93 through 102 )
35X-RAY DIFFRACTION35chain 'F' and (resid 103 through 115 )
36X-RAY DIFFRACTION36chain 'F' and (resid 116 through 134 )
37X-RAY DIFFRACTION37chain 'F' and (resid 135 through 167 )

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