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- PDB-6yaz: Crystal structure of a parallel hexameric coiled coil CC-Type2-(TaId)5 -

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Basic information

Entry
Database: PDB / ID: 6yaz
TitleCrystal structure of a parallel hexameric coiled coil CC-Type2-(TaId)5
ComponentsCC-Type2-(TaId)5
KeywordsDE NOVO PROTEIN / alpha-helical barrel / de novo peptide / coiled coil / designed peptide / designed protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsScott, A.J. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council (ERC)340764 United Kingdom
European Research Council (ERC)787173 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J009784/1 United Kingdom
CitationJournal: Nat.Chem. / Year: 2021
Title: Constructing ion channels from water-soluble alpha-helical barrels.
Authors: Scott, A.J. / Niitsu, A. / Kratochvil, H.T. / Lang, E.J.M. / Sengel, J.T. / Dawson, W.M. / Mahendran, K.R. / Mravic, M. / Thomson, A.R. / Brady, R.L. / Liu, L. / Mulholland, A.J. / Bayley, H. ...Authors: Scott, A.J. / Niitsu, A. / Kratochvil, H.T. / Lang, E.J.M. / Sengel, J.T. / Dawson, W.M. / Mahendran, K.R. / Mravic, M. / Thomson, A.R. / Brady, R.L. / Liu, L. / Mulholland, A.J. / Bayley, H. / DeGrado, W.F. / Wallace, M.I. / Woolfson, D.N.
History
DepositionMar 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(TaId)5
B: CC-Type2-(TaId)5
C: CC-Type2-(TaId)5
D: CC-Type2-(TaId)5
E: CC-Type2-(TaId)5
F: CC-Type2-(TaId)5
G: CC-Type2-(TaId)5
H: CC-Type2-(TaId)5
I: CC-Type2-(TaId)5
J: CC-Type2-(TaId)5
K: CC-Type2-(TaId)5
L: CC-Type2-(TaId)5


Theoretical massNumber of molelcules
Total (without water)47,15412
Polymers47,15412
Non-polymers00
Water2,126118
1
A: CC-Type2-(TaId)5
B: CC-Type2-(TaId)5
C: CC-Type2-(TaId)5
D: CC-Type2-(TaId)5
E: CC-Type2-(TaId)5
F: CC-Type2-(TaId)5


Theoretical massNumber of molelcules
Total (without water)23,5776
Polymers23,5776
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-107 kcal/mol
Surface area11400 Å2
MethodPISA
2
G: CC-Type2-(TaId)5
H: CC-Type2-(TaId)5
I: CC-Type2-(TaId)5
J: CC-Type2-(TaId)5
K: CC-Type2-(TaId)5
L: CC-Type2-(TaId)5


Theoretical massNumber of molelcules
Total (without water)23,5776
Polymers23,5776
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-103 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.136, 43.307, 83.024
Angle α, β, γ (deg.)101.530, 97.690, 90.210
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 through 7 and (name N...
21(chain B and ((resid 2 through 7 and (name N...
31(chain C and ((resid 2 through 7 and (name N...
41(chain D and ((resid 2 through 7 and (name N...
51(chain E and ((resid 2 through 7 and (name N...
61(chain F and ((resid 2 through 7 and (name N...
71(chain G and ((resid 2 through 7 and (name N...
81(chain H and ((resid 2 through 7 and (name N...
91(chain I and ((resid 2 through 7 and (name N...
101(chain J and ((resid 2 through 7 and (name N...
111(chain K and ((resid 2 through 7 and (name N...
121(chain L and ((resid 2 through 7 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTHRTHR(chain A and ((resid 2 through 7 and (name N...AA2 - 73 - 8
12GLYGLYLYSLYS(chain A and ((resid 2 through 7 and (name N...AA1 - 362 - 37
13GLYGLYLYSLYS(chain A and ((resid 2 through 7 and (name N...AA1 - 362 - 37
14GLYGLYLYSLYS(chain A and ((resid 2 through 7 and (name N...AA1 - 362 - 37
15GLYGLYLYSLYS(chain A and ((resid 2 through 7 and (name N...AA1 - 362 - 37
21GLUGLUTHRTHR(chain B and ((resid 2 through 7 and (name N...BB2 - 73 - 8
22GLYGLYLYSLYS(chain B and ((resid 2 through 7 and (name N...BB1 - 362 - 37
23GLYGLYLYSLYS(chain B and ((resid 2 through 7 and (name N...BB1 - 362 - 37
24GLYGLYLYSLYS(chain B and ((resid 2 through 7 and (name N...BB1 - 362 - 37
25GLYGLYLYSLYS(chain B and ((resid 2 through 7 and (name N...BB1 - 362 - 37
31GLUGLUTHRTHR(chain C and ((resid 2 through 7 and (name N...CC2 - 73 - 8
32GLYGLYLYSLYS(chain C and ((resid 2 through 7 and (name N...CC1 - 362 - 37
33GLYGLYLYSLYS(chain C and ((resid 2 through 7 and (name N...CC1 - 362 - 37
34GLYGLYLYSLYS(chain C and ((resid 2 through 7 and (name N...CC1 - 362 - 37
35GLYGLYLYSLYS(chain C and ((resid 2 through 7 and (name N...CC1 - 362 - 37
41GLUGLUTHRTHR(chain D and ((resid 2 through 7 and (name N...DD2 - 73 - 8
42GLYGLYLYSLYS(chain D and ((resid 2 through 7 and (name N...DD1 - 362 - 37
43GLYGLYLYSLYS(chain D and ((resid 2 through 7 and (name N...DD1 - 362 - 37
44GLYGLYLYSLYS(chain D and ((resid 2 through 7 and (name N...DD1 - 362 - 37
45GLYGLYLYSLYS(chain D and ((resid 2 through 7 and (name N...DD1 - 362 - 37
51GLUGLUTHRTHR(chain E and ((resid 2 through 7 and (name N...EE2 - 73 - 8
52GLYGLYGLYGLY(chain E and ((resid 2 through 7 and (name N...EE1 - 372 - 38
53GLYGLYGLYGLY(chain E and ((resid 2 through 7 and (name N...EE1 - 372 - 38
54GLYGLYGLYGLY(chain E and ((resid 2 through 7 and (name N...EE1 - 372 - 38
55GLYGLYGLYGLY(chain E and ((resid 2 through 7 and (name N...EE1 - 372 - 38
61GLUGLUTHRTHR(chain F and ((resid 2 through 7 and (name N...FF2 - 73 - 8
62GLYGLYLYSLYS(chain F and ((resid 2 through 7 and (name N...FF1 - 362 - 37
63GLYGLYLYSLYS(chain F and ((resid 2 through 7 and (name N...FF1 - 362 - 37
64GLYGLYLYSLYS(chain F and ((resid 2 through 7 and (name N...FF1 - 362 - 37
65GLYGLYLYSLYS(chain F and ((resid 2 through 7 and (name N...FF1 - 362 - 37
71GLUGLUTHRTHR(chain G and ((resid 2 through 7 and (name N...GG2 - 73 - 8
72GLYGLYLYSLYS(chain G and ((resid 2 through 7 and (name N...GG1 - 362 - 37
73GLYGLYLYSLYS(chain G and ((resid 2 through 7 and (name N...GG1 - 362 - 37
74GLYGLYLYSLYS(chain G and ((resid 2 through 7 and (name N...GG1 - 362 - 37
75GLYGLYLYSLYS(chain G and ((resid 2 through 7 and (name N...GG1 - 362 - 37
81GLUGLUTHRTHR(chain H and ((resid 2 through 7 and (name N...HH2 - 73 - 8
82GLYGLYLYSLYS(chain H and ((resid 2 through 7 and (name N...HH1 - 362 - 37
83GLYGLYLYSLYS(chain H and ((resid 2 through 7 and (name N...HH1 - 362 - 37
84GLYGLYLYSLYS(chain H and ((resid 2 through 7 and (name N...HH1 - 362 - 37
85GLYGLYLYSLYS(chain H and ((resid 2 through 7 and (name N...HH1 - 362 - 37
91GLUGLUTHRTHR(chain I and ((resid 2 through 7 and (name N...II2 - 73 - 8
92GLYGLYLYSLYS(chain I and ((resid 2 through 7 and (name N...II1 - 362 - 37
93GLYGLYLYSLYS(chain I and ((resid 2 through 7 and (name N...II1 - 362 - 37
94GLYGLYLYSLYS(chain I and ((resid 2 through 7 and (name N...II1 - 362 - 37
95GLYGLYLYSLYS(chain I and ((resid 2 through 7 and (name N...II1 - 362 - 37
101GLUGLUTHRTHR(chain J and ((resid 2 through 7 and (name N...JJ2 - 73 - 8
102GLYGLYLYSLYS(chain J and ((resid 2 through 7 and (name N...JJ1 - 362 - 37
103GLYGLYLYSLYS(chain J and ((resid 2 through 7 and (name N...JJ1 - 362 - 37
104GLYGLYLYSLYS(chain J and ((resid 2 through 7 and (name N...JJ1 - 362 - 37
105GLYGLYLYSLYS(chain J and ((resid 2 through 7 and (name N...JJ1 - 362 - 37
111GLUGLUTHRTHR(chain K and ((resid 2 through 7 and (name N...KK2 - 73 - 8
112GLYGLYLYSLYS(chain K and ((resid 2 through 7 and (name N...KK1 - 362 - 37
113GLYGLYLYSLYS(chain K and ((resid 2 through 7 and (name N...KK1 - 362 - 37
114GLYGLYLYSLYS(chain K and ((resid 2 through 7 and (name N...KK1 - 362 - 37
115GLYGLYLYSLYS(chain K and ((resid 2 through 7 and (name N...KK1 - 362 - 37
121GLUGLUTHRTHR(chain L and ((resid 2 through 7 and (name N...LL2 - 73 - 8
122GLYGLYLYSLYS(chain L and ((resid 2 through 7 and (name N...LL1 - 362 - 37
123GLYGLYLYSLYS(chain L and ((resid 2 through 7 and (name N...LL1 - 362 - 37
124GLYGLYLYSLYS(chain L and ((resid 2 through 7 and (name N...LL1 - 362 - 37
125GLYGLYLYSLYS(chain L and ((resid 2 through 7 and (name N...LL1 - 362 - 37

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Components

#1: Protein/peptide
CC-Type2-(TaId)5


Mass: 3929.494 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaNO3, 0.05 M Bis-Tris propane, 10% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→40.3 Å / Num. obs: 39971 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.7
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1922 / CC1/2: 0.516 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Parametric Model

Resolution: 1.94→40.29 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.66
RfactorNum. reflection% reflection
Rfree0.2317 1964 5.04 %
Rwork0.2103 --
obs0.2115 38966 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.82 Å2 / Biso mean: 60.0385 Å2 / Biso min: 16.41 Å2
Refinement stepCycle: final / Resolution: 1.94→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 0 118 3350
Biso mean---56.47 -
Num. residues----433
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A946X-RAY DIFFRACTION9.124TORSIONAL
12B946X-RAY DIFFRACTION9.124TORSIONAL
13C946X-RAY DIFFRACTION9.124TORSIONAL
14D946X-RAY DIFFRACTION9.124TORSIONAL
15E946X-RAY DIFFRACTION9.124TORSIONAL
16F946X-RAY DIFFRACTION9.124TORSIONAL
17G946X-RAY DIFFRACTION9.124TORSIONAL
18H946X-RAY DIFFRACTION9.124TORSIONAL
19I946X-RAY DIFFRACTION9.124TORSIONAL
110J946X-RAY DIFFRACTION9.124TORSIONAL
111K946X-RAY DIFFRACTION9.124TORSIONAL
112L946X-RAY DIFFRACTION9.124TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.990.44771120.41661996210873
1.99-2.040.3211260.32172618274495
2.04-2.10.34731350.30822605274096
2.1-2.170.31931250.26812706283199
2.17-2.250.28841330.26522720285398
2.25-2.340.3561040.26862696280098
2.34-2.440.27541240.223627572881100
2.44-2.570.23871450.202327272872100
2.57-2.730.2121660.183226812847100
2.73-2.940.25691550.202127282883100
2.94-3.240.26051350.197627322867100
3.24-3.710.23421950.207826962891100
3.71-4.670.2011580.16732668282699
4.67-40.290.17371510.20532672282397
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)
11.34260.19610.03021.2519-0.92920.6293-0.09480.2531-0.0578-0.0830.11530.37910.4732-0.1952-00.2912-0.017-0.04070.3261-0.01760.377-7.8895-2.420428.1858
22.0055-0.41931.04462.0345-0.86310.6561-0.21290.3389-0.3411-0.2045-0.16690.2970.8430.0597-0.00560.32950.002-0.02120.3142-0.05050.3743-2.6492-8.461327.7182
32.7179-0.53761.22651.5990.60890.881-0.03460.4483-0.2104-0.47040.2236-0.07160.60690.2651-0.00080.33280.00360.04780.3683-0.0650.40855.2964-6.338527.4766
42.4038-0.00230.48191.93871.15450.67140.04610.3992-0.0664-0.2285-0.0502-0.1339-0.34170.9847-0.00010.2788-0.03110.02940.3248-0.01670.35267.38631.445927.3431
50.78970.0016-0.51661.99710.96240.5493-0.33740.2890.2086-0.3482-0.183-0.1094-0.51430.1675-0.0080.3773-0.039-0.00540.32070.0510.30062.19927.025127.8404
61.9306-0.7515-0.94741.0081-0.31210.8236-0.28440.2960.2733-0.5417-0.23080.5095-0.8155-0.5761-0.00910.34830.0341-0.08930.28950.01920.298-5.93584.904426.9503
70.9776-0.2379-0.56881.941-0.72450.533-0.3576-0.44960.44270.3295-0.07970.0646-0.74690.0908-00.39080.0343-0.01020.4028-0.07320.345917.591328.576455.2241
81.92420.8647-1.1510.95260.21260.9843-0.1712-0.30240.36890.4290.0212-0.2636-0.57640.196-0.01140.34070.0002-0.0440.3547-0.06850.31925.197626.498855.1028
91.8452-0.0949-0.56791.8271.15130.725-0.0985-0.30630.06940.35960.0079-0.41360.45130.468-0.00340.36870.0407-0.05870.35790.00020.356427.3618.844254.95
101.94490.15591.04852.37050.76350.7772-0.1719-0.4684-0.42970.2786-0.3069-0.19890.66560.1765-0.00850.3484-0.0185-0.02040.29710.06220.311321.780313.281355.0876
112.26120.41260.93461.379-0.52640.86190.0242-0.3984-0.25910.36260.10350.07010.7572-0.20350.0270.2906-0.06030.05760.33980.07740.305314.068615.341955.0866
121.8792-0.14110.32291.2097-0.92720.657-0.1468-0.3526-0.01390.0916-0.05870.2021-0.368-0.5297-0.00070.26490.01420.03250.29940.0020.241412.030223.055154.9344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:36)A1 - 36
2X-RAY DIFFRACTION2(chain B and resseq 1:36)B1 - 36
3X-RAY DIFFRACTION3(chain C and resseq 1:36)C1 - 36
4X-RAY DIFFRACTION4(chain D and resseq 1:36)D1 - 36
5X-RAY DIFFRACTION5(chain E and resseq 1:37)E1 - 37
6X-RAY DIFFRACTION6(chain F and resseq 1:36)F1 - 36
7X-RAY DIFFRACTION7(chain G and resseq 1:36)G1 - 36
8X-RAY DIFFRACTION8(chain H and resseq 1:36)H1 - 36
9X-RAY DIFFRACTION9(chain I and resseq 1:36)I1 - 36
10X-RAY DIFFRACTION10(chain J and resseq 1:36)J1 - 36
11X-RAY DIFFRACTION11(chain K and resseq 1:36)K1 - 36
12X-RAY DIFFRACTION12(chain L and resseq 1:36)L1 - 36

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