[English] 日本語
Yorodumi
- PDB-7q1r: A de novo designed homo-dimeric antiparallel coiled coil apCC-Di -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q1r
TitleA de novo designed homo-dimeric antiparallel coiled coil apCC-Di
ComponentsapCC-Di
KeywordsDE NOVO PROTEIN / antiparallel / homo-dimeric / coiled-coil / de novo / protein design / associating peptides
Function / homologyETHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsShanmugaratnam, S. / Rhys, G.G. / Dawson, W.M. / Woolfson, D.N. / Hocker, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission888993European Union
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: De novo designed peptides for cellular delivery and subcellular localisation.
Authors: Rhys, G.G. / Cross, J.A. / Dawson, W.M. / Thompson, H.F. / Shanmugaratnam, S. / Savery, N.J. / Dodding, M.P. / Hocker, B. / Woolfson, D.N.
History
DepositionOct 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 31, 2022Group: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: apCC-Di
B: apCC-Di
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8774
Polymers6,8082
Non-polymers692
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-21 kcal/mol
Surface area4850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.096, 35.096, 92.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-101-

EOH

21A-201-

HOH

31B-231-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 4 or resid 7 through 10 or resid 12 or resid 14 through 31))
d_2ens_1(chain "B" and (resid 1 through 4 or resid 7 through 10 or resid 12 or resid 14 through 31))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLUA1 - 4
d_12ens_1LEULEUA7 - 10
d_13ens_1GLNGLNA12
d_14ens_1ILEGLYA14 - 30
d_21ens_1GLYGLUE2 - 5
d_22ens_1LEULEUE8 - 11
d_23ens_1GLNGLNE13
d_24ens_1ILEGLYE15 - 31

NCS oper: (Code: givenMatrix: (0.987687711141, -0.153601000311, 0.0296600398479), (-0.153557789067, -0.988132580609, -0.00374280043753), (0.0298829496071, -0.000857812145288, -0.999553036853)Vector: - ...NCS oper: (Code: given
Matrix: (0.987687711141, -0.153601000311, 0.0296600398479), (-0.153557789067, -0.988132580609, -0.00374280043753), (0.0298829496071, -0.000857812145288, -0.999553036853)
Vector: -0.286868951925, 2.78972688728, 18.742491002)

-
Components

#1: Protein/peptide apCC-Di


Mass: 3403.910 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% ethanol, 1.5 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.08→27.95 Å / Num. obs: 25670 / % possible obs: 99.6 % / Redundancy: 10.6 % / Biso Wilson estimate: 14.52 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Net I/σ(I): 64.93
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.612 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 2505 / CC1/2: 0.33 / CC star: 0.705 / Rpim(I) all: 0.533 / Rrim(I) all: 1.701 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS2.0.2data reduction
DIALS2.0.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanine coiled-coil

Resolution: 1.08→27.95 Å / SU ML: 0.1326 / Cross valid method: FREE R-VALUE / Phase error: 24.3192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2168 1283 5.01 %
Rwork0.1892 24313 -
obs0.1906 25596 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.18 Å2
Refinement stepCycle: LAST / Resolution: 1.08→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 9 93 576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0105511
X-RAY DIFFRACTIONf_angle_d0.9428688
X-RAY DIFFRACTIONf_chiral_restr0.059974
X-RAY DIFFRACTIONf_plane_restr0.009694
X-RAY DIFFRACTIONf_dihedral_angle_d20.3522204
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.04734470194 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.120.34821390.34832638X-RAY DIFFRACTION99.46
1.12-1.170.2851400.27832621X-RAY DIFFRACTION99.07
1.17-1.240.26061390.2622637X-RAY DIFFRACTION99.28
1.24-1.310.25111390.24182659X-RAY DIFFRACTION99.89
1.31-1.420.26411420.22652682X-RAY DIFFRACTION99.86
1.42-1.560.22011400.19342665X-RAY DIFFRACTION99.26
1.56-1.780.19291450.18082731X-RAY DIFFRACTION99.86
1.78-2.250.19081450.1742751X-RAY DIFFRACTION99.9
2.25-27.950.21121540.17182929X-RAY DIFFRACTION99.84
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)
10.9394789352030.2125289620110.4806428327741.70042190421-0.7061207695680.809584217665-0.09889537017420.0112540833893-0.04216945369380.0914397751191-0.0087005286388-0.008193777641070.186015047425-0.101821228246-0.003723456371470.0632048367615-0.0110093974057-0.003122829318910.08655998633520.006630218256230.09953435383710.9836332776-3.3166993899310.8476569944
20.769133621976-0.3059215165470.1405229224291.45538444998-0.05792998587482.50399734668-0.0290739774301-0.03606254611690.00777610116826-0.0589680368450.0682772961046-0.0776219574224-0.172783105251-0.1397286772920.05966374643960.08824518109520.01184902986570.003670950226460.125732426995-2.94557878772E-50.13280938674611.26590320144.292474135857.63809284874
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 31)AA - B1 - 311
22(chain 'B' and resid 0 through 31)BD - F0 - 31

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more