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- PDB-9evg: X-ray crystal structure of a de novo designed parallel coiled-coi... -

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Basic information

Entry
Database: PDB / ID: 9evg
TitleX-ray crystal structure of a de novo designed parallel coiled-coil heterohexamer with 3 heptad repeats, CCHex2-AB-g
Components
  • CCHex2-A-g
  • CCHex2-B-g
KeywordsDE NOVO PROTEIN / COILED COIL / HETEROMER / 6-HELIX BARREL / DE NOVO PROTEIN DESIGN / PEPTIDE ASSEMBLY
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å
AuthorsAlbanese, K.I. / Chubb, J.J. / Woolfson, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Biochemistry / Year: 2025
Title: De Novo Design of Parallel and Antiparallel A 3 B 3 Heterohexameric alpha-Helical Barrels.
Authors: Chubb, J.J. / Albanese, K.I. / Rodger, A. / Woolfson, D.N.
History
DepositionMar 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: CCHex2-B-g
B: CCHex2-A-g
H: CCHex2-B-g
J: CCHex2-A-g
I: CCHex2-A-g
K: CCHex2-B-g
L: CCHex2-A-g
A: CCHex2-B-g
D: CCHex2-A-g
C: CCHex2-A-g
F: CCHex2-B-g
E: CCHex2-B-g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,78015
Polymers30,19812
Non-polymers5833
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, 6x monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.676, 94.612, 51.116
Angle α, β, γ (deg.)90.000, 91.750, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 21 or (resid 22...
d_2ens_1(chain "E" and (resid 0 through 4 or (resid 5...
d_3ens_1(chain "F" and (resid 0 through 10 or (resid 11...
d_4ens_1(chain "G" and (resid 0 through 7 or (resid 8...
d_5ens_1(chain "H" and (resid 0 through 4 or (resid 5...
d_6ens_1(chain "K" and (resid 0 through 3 or (resid 4...
d_1ens_2(chain "B" and (resid 0 through 4 or (resid 5...
d_2ens_2(chain "C" and (resid 0 through 4 or (resid 5...
d_3ens_2(chain "D" and (resid 0 through 4 or (resid 5...
d_4ens_2(chain "I" and (resid 0 through 4 or (resid 5...
d_5ens_2(chain "J" and (resid 0 through 7 or (resid 8...
d_6ens_2(chain "L" and (resid 0 through 4 or (resid 5...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ACEACEACEACEAH01
d_12ens_1GLYGLYGLNGLNAH1 - 222 - 23
d_21ens_1ACEACEACEACEEL01
d_22ens_1GLYGLYGLNGLNEL1 - 222 - 23
d_31ens_1ACEACEACEACEFK01
d_32ens_1GLYGLYGLNGLNFK1 - 222 - 23
d_41ens_1ACEACEACEACEGA01
d_42ens_1GLYGLYGLNGLNGA1 - 222 - 23
d_51ens_1ACEACEACEACEHC01
d_52ens_1GLYGLYGLNGLNHC1 - 222 - 23
d_61ens_1ACEACEACEACEKF01
d_62ens_1GLYGLYGLNGLNKF1 - 222 - 23
d_11ens_2ACEACEACEACEBB01
d_12ens_2GLYGLYGLNGLNBB1 - 222 - 23
d_21ens_2ACEACEACEACECJ01
d_22ens_2GLYGLYGLNGLNCJ1 - 222 - 23
d_31ens_2ACEACEACEACEDI01
d_32ens_2GLYGLYGLNGLNDI1 - 222 - 23
d_41ens_2ACEACEACEACEIE01
d_42ens_2GLYGLYGLNGLNIE1 - 222 - 23
d_51ens_2ACEACEACEACEJD01
d_52ens_2GLYGLYGLNGLNJD1 - 222 - 23
d_61ens_2ACEACEACEACELG01
d_62ens_2GLYGLYGLNGLNLG1 - 222 - 23

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.448325169367, -0.450840259889, 0.771846877675), (-0.0768973817063, 0.879739909041, 0.469195572366), (-0.890556755743, 0.150999180476, -0.429077979272)65.2051743304, 12.923364084, -1.66917759407
2given(-0.418884293961, -0.0659624845553, -0.9056406014), (-0.458202945928, 0.876422975999, 0.148097358124), (0.783955361367, 0.477002848809, -0.397344024257)27.4766650075, 18.570171285, -57.0797112416
3given(0.35463324673, 0.0756274923625, 0.931941920247), (0.0848499690468, -0.995213925818, 0.0484739580702), (0.931147540976, 0.061884765954, -0.35935293609)24.4838083097, 82.1734414579, -42.9454190614
4given(0.550929044986, 0.480357495253, -0.682446968009), (0.446684188846, -0.860474432767, -0.245065268836), (-0.704947106403, -0.169824695816, -0.688628455603)-17.3687136061, 63.6573534182, 4.19504409102
5given(-0.993870678769, 0.0252021801553, -0.107637930115), (0.0269358880683, -0.889116394858, -0.45688783561), (-0.107217217918, -0.456986746537, 0.882987871758)47.3364421326, 73.0154335831, 20.2019807296
6given(-0.451853513223, -0.0875389729642, -0.887786759757), (-0.465230747469, 0.872253354235, 0.15077943373), (0.761175902271, 0.481155914687, -0.434856564356)29.1672357444, 18.8883081023, -57.2254674961
7given(-0.465956601219, -0.447227987055, 0.763460263128), (-0.0818686603608, 0.880944940741, 0.466083183384), (-0.881011900165, 0.154671067034, -0.447096066624)65.6072127653, 12.9855006918, -2.47679539709
8given(0.325704333382, 0.0609186177043, 0.943507079588), (0.0691068410169, -0.996786730166, 0.0405025812619), (0.942942698016, 0.0520109275172, -0.328867650701)26.2512634535, 82.6405988074, -42.5919313736
9given(-0.995715943406, 0.0401022724813, -0.0833160716168), (-0.00269896552377, -0.913277292589, -0.4073294765), (-0.0924255139717, -0.405359586765, 0.909472995633)47.2770917358, 75.2260100056, 18.534595397
10given(0.507798927064, 0.480551306558, -0.714989993943), (0.472223225855, -0.849430200885, -0.235528254755), (-0.720517504739, -0.218033886336, -0.658267232796)-16.9160008437, 62.7507810687, 6.40693645726

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Components

#1: Protein/peptide
CCHex2-B-g


Mass: 2505.139 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide
CCHex2-A-g


Mass: 2527.779 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Sodium HEPES 7.5 20 % v/v Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→47.31 Å / Num. obs: 24363 / % possible obs: 99.87 % / Redundancy: 13.2 % / Biso Wilson estimate: 29.29 Å2 / CC1/2: 0.997 / CC star: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.03329 / Rrim(I) all: 0.1189 / Net I/σ(I): 11.57
Reflection shellResolution: 1.9→1.971 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.2568 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 2402 / CC1/2: 0.975 / CC star: 0.994 / Rpim(I) all: 0.0735 / Rrim(I) all: 0.2673 / % possible all: 99.26

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→47.31 Å / SU ML: 0.2417 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 22.2662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 1134 4.66 %
Rwork0.1997 23216 -
obs0.2009 24350 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 79 79 1911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231825
X-RAY DIFFRACTIONf_angle_d0.56612451
X-RAY DIFFRACTIONf_chiral_restr0.0332324
X-RAY DIFFRACTIONf_plane_restr0.0025293
X-RAY DIFFRACTIONf_dihedral_angle_d16.5059310
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2VLX-RAY DIFFRACTIONTorsion NCS0.235052674814
ens_1d_3VLX-RAY DIFFRACTIONTorsion NCS0.488548109919
ens_1d_4VLX-RAY DIFFRACTIONTorsion NCS0.449093012307
ens_1d_5VLX-RAY DIFFRACTIONTorsion NCS0.529344383436
ens_1d_6VLX-RAY DIFFRACTIONTorsion NCS0.492267465013
ens_2d_2NLX-RAY DIFFRACTIONTorsion NCS0.178319152179
ens_2d_3NLX-RAY DIFFRACTIONTorsion NCS0.211493345158
ens_2d_4NLX-RAY DIFFRACTIONTorsion NCS0.223352535902
ens_2d_5NLX-RAY DIFFRACTIONTorsion NCS0.229290932218
ens_2d_6NLX-RAY DIFFRACTIONTorsion NCS0.491669998069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.30841320.24192877X-RAY DIFFRACTION99.41
1.99-2.090.25531700.21392869X-RAY DIFFRACTION100
2.09-2.230.21241430.18942894X-RAY DIFFRACTION100
2.23-2.40.1981320.17972919X-RAY DIFFRACTION100
2.4-2.640.25711340.22889X-RAY DIFFRACTION100
2.64-3.020.24861320.20692932X-RAY DIFFRACTION100
3.02-3.80.23571240.2052911X-RAY DIFFRACTION99.97
3.8-47.310.2021670.19262925X-RAY DIFFRACTION99.61
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)
14.819296155382.90403566570.2095669144829.341908342912.419168297342.11666546407-0.2370960952280.1878917203240.331864138384-0.5614431829660.3368283565420.680676182414-0.1815447522080.183440793227-0.1324635258810.2347081932190.0237851097142-0.04578900722130.2842135233870.001767586254870.2534603997417.313102041458.9639940047-17.028521077
26.17172119236-6.22854117168-3.798348334738.798668935214.965364533259.03248602854-0.2149159053820.0264614573880.0300980794350.2213474152330.0441787441195-0.08088402968860.05305283036590.5021744784620.01926812751130.170440766611-0.0204000398097-0.01732164436510.313548522905-7.56421961337E-70.27648565858337.214565340627.0094311782-15.1057496301
34.90169455739-1.58356365122.602858214235.61987884631-3.507494516143.993139084-0.0396358458644-0.5365584303670.2163006300040.5394423160860.1724731593450.485776388391-0.115117687212-0.268171777325-0.05493697631320.26957555325-0.03401239841030.06648985048110.315398484886-0.03543796811930.20642543172916.498186021356.455197383-1.81123247583
47.23878473551-4.720746420191.29603160933.93673569501-3.01528251515.71905948855-0.345252870631-0.0473375942050.198474670689-0.02775328544050.367671333061-0.2336817221090.0482895541244-0.30390482579-0.02842998729290.205139267243-0.03850821120610.02864185663620.277536023716-0.02258213147360.26134849930513.14872487555.8503125855-9.47583526589
57.54670252411-2.23445039587-4.194789443478.93732969214.465973204044.783576165670.231403117202-0.587798834717-0.02481216750820.312329328914-0.0162042817913-0.399402919215-0.04219212062370.125431180423-0.3927160552730.2796570788060.00873007790512-0.08702735484690.285921861259-0.03035379144360.23938522864625.569933765757.4663126663-1.64863675401
65.17567133338-1.76855680192-1.668108447756.745419137772.043856229785.171583107650.0144605900545-0.214293089381-0.007106749717420.318549343849-0.00806651569873-0.601561326068-0.1999331181810.183480996569-0.0316109932010.160087613473-0.0257588932177-0.05630907138610.260035621468-0.002008392740680.24241912162530.268025660860.2165762388-7.95074126134
74.574166980813.20407597374-0.3385342079773.004092802611.669458943257.11582071901-0.3171951148790.08376508950820.289024357454-0.2596321877240.3955566010370.820613588821-0.2052892870040.381521798127-0.152583911910.184897571890.02959848906620.01067052916410.3012417312260.00119661324990.19275824095725.446565747760.0506840199-16.4410818098
84.41454526004-3.254523128662.056998287872.54971970543-1.303804392423.90735745292-0.14092464887-0.0262555336017-0.42039688211-0.3610849879120.2699062772750.4238700149930.269983848244-0.165167564297-0.1058351470320.210396340088-0.02136018125440.05342767606510.281449927007-0.01448282460490.29570118124419.780359748523.6498014949-17.1226539707
95.48569084750.4525010973230.3884054933326.09269644041-0.8944298243294.45636826490.03865794479760.415675365984-0.180248595350.0390543091830.1568991770110.1498868645210.1301639248330.0116179391651-0.1450595918990.201016422988-0.007453160978410.01565460444080.308108368943-0.03581937287540.21698300811124.415501375926.710563269-24.3815330611
109.02971370699-4.821120959810.7877107193032.72371357017-1.008662309983.8235554161-0.298209772653-0.543607796472-0.6344970002550.3925040145670.3406557907040.4247902108860.1521918485020.0118869526681-0.0598762169860.2564384835190.02539100113850.07224954804990.3095409067480.03656876747360.25883178389723.764396337822.6381885884-9.07285428655
116.60939142588-0.7512025620950.8516327688599.39929329545.996688850666.98802142999-0.07238371204450.5874260418650.103147923705-0.1024024661880.07940634677120.0606446139384-0.004896127594340.371289022342-0.08936261465530.1333790332160.01687462748930.03034230765770.31989007950.003922413300310.19830833466733.266359001428.140826595-23.2953265677
125.7646079119-4.0839089509-2.078079595657.196553670551.948158351567.4686932372-0.423930953602-0.143488051305-0.09268816091530.7895256257640.223864418634-0.04145931315080.1025957419520.09549128043680.2125248945120.2757081721050.0292117019511-0.02093921803910.2502777239050.01263596760330.24834373025531.806962637225.0852305598-7.86988599839
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDEnd label seq-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1231(chain 'G' and resid 0 through 22)GA0 - 22
2242(chain 'B' and resid 0 through 23)BB0 - 23
3243(chain 'H' and resid 0 through 23)HC0 - 23
4234(chain 'J' and resid 0 through 22)JD0 - 22
5245(chain 'I' and resid 0 through 23)IE0 - 23
6246(chain 'K' and resid 0 through 23)KF0 - 23
7237(chain 'L' and resid 0 through 22)LG0 - 22
8248(chain 'A' and resid 0 through 23)AH0 - 23
9239(chain 'D' and resid 0 through 22)DI0 - 22
102410(chain 'C' and resid 0 through 23)CJ0 - 23
112411(chain 'F' and resid 0 through 23)FK0 - 23
122312(chain 'E' and resid 0 through 22)EL0 - 22

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