[English] 日本語
Yorodumi
- PDB-7q1t: A de novo designed hetero-dimeric antiparallel coiled coil apCC-Di-AB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q1t
TitleA de novo designed hetero-dimeric antiparallel coiled coil apCC-Di-AB
Components
  • apCC-Di-A
  • apCC-Di-B
KeywordsDE NOVO PROTEIN / antiparallel / hetero-dimeric / coiled-coil / de novo / protein design / associating peptides
Function / homologyN-PROPANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,9645
Polymers6,7482
Non-polymers2163
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-17 kcal/mol
Surface area4560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.219, 47.219, 70.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-127-

HOH

21B-247-

HOH

-
Components

#1: Protein/peptide apCC-Di-A


Mass: 3252.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide apCC-Di-B


Mass: 3495.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M lithium sulfate, 0.1M phosphate citrate pH 4.2, 10% isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2021
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: 1.68→24.19 Å / Num. obs: 8726 / % possible obs: 98.3 % / Redundancy: 10.5 % / Biso Wilson estimate: 29.45 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.415 / Rpim(I) all: 0.135 / Rrim(I) all: 0.437 / Net I/σ(I): 30.55
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.587 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 854 / CC1/2: 0.269 / CC star: 0.652 / Rpim(I) all: 0.531 / Rrim(I) all: 1.678 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
DIALS2.0.2data reduction
DIALS2.0.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanine coiled-coil

Resolution: 1.68→24.19 Å / SU ML: 0.2522 / Cross valid method: FREE R-VALUE / Phase error: 35.0697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2211 906 10.48 %
Rwork0.1864 7740 -
obs0.19 8646 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.03 Å2
Refinement stepCycle: LAST / Resolution: 1.68→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 13 75 562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016509
X-RAY DIFFRACTIONf_angle_d0.3221681
X-RAY DIFFRACTIONf_chiral_restr0.023172
X-RAY DIFFRACTIONf_plane_restr0.001991
X-RAY DIFFRACTIONf_dihedral_angle_d18.3963204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.790.3847890.353841X-RAY DIFFRACTION97.47
1.79-1.920.29711490.26181305X-RAY DIFFRACTION99.38
1.92-2.120.25531460.21821277X-RAY DIFFRACTION97.73
2.12-2.420.21721490.19061308X-RAY DIFFRACTION99.66
2.42-3.050.20451490.18711281X-RAY DIFFRACTION97.54
3.05-24.190.20391590.16071299X-RAY DIFFRACTION98.12
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)
10.778126961112-0.208059324116-0.3099621587441.32761669668-0.2470063692982.757917461640.29838535790.2702196021750.130798995565-0.315396129669-0.182071415170.01918960456750.270775186958-0.0963953589806-3.1465638914E-50.324491159157-0.0626441294175-0.02454448212980.223133622664-0.001141627618890.229336517360.0272023571402-4.986748753119.10303961215
20.76064413184-1.22912829596-0.5703646287962.81976495351-0.1985893952513.27669298668-0.03492649917570.0482782304657-0.397656982662-0.2679027083610.1573011236940.2493417049570.2850167984690.08638059666170.0003958755654760.343271969641-0.0805946341822-0.02203464954920.258648354980.05361263032470.2726107955870.302904634065-9.465419172816.8241451245
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 30 / Label seq-ID: 1 - 30

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 1 through 30)AA
22(chain 'B' and resid 1 through 30)BC

+
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