[English] 日本語
Yorodumi
- PDB-9tll: De novo designed single-chain antiparallel coiled-coil hairpin, S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9tll
TitleDe novo designed single-chain antiparallel coiled-coil hairpin, Sc-apCC-2
ComponentsSc-apCC-2
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMylemans, B. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006703/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/2 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: De Novo-Designed Bifunctional
Authors: Mylemans, B. / Korona, B. / Acevedo-Jake, A.M. / MacRae, A. / Edwards, T.A. / Huang, D.T. / Wilson, A.J. / Itzhaki, L.S. / Woolfson, D.N.
History
DepositionDec 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sc-apCC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4318
Polymers7,7571
Non-polymers6757
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.237, 48.237, 70.272
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

#1: Protein Sc-apCC-2


Mass: 7756.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 48 / 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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Lithium sulfate, 0.1 M Phosphate/citrate, 20% w/v PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.5→34.11 Å / Num. obs: 15585 / % possible obs: 99.44 % / Redundancy: 11.6 % / Biso Wilson estimate: 13.69 Å2 / CC1/2: 0.95 / Net I/σ(I): 11.04
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 1237 / CC1/2: 0.11 / CC star: 0.44 / Rpim(I) all: 0.84 / % possible all: 97.25

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.11 Å / SU ML: 0.1146 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 617 4.82 %
Rwork0.1809 12191 -
obs0.1816 12808 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.44 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 42 48 610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086580
X-RAY DIFFRACTIONf_angle_d1.0669780
X-RAY DIFFRACTIONf_chiral_restr0.039382
X-RAY DIFFRACTIONf_plane_restr0.0073100
X-RAY DIFFRACTIONf_dihedral_angle_d15.6042227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.650.22631360.17983015X-RAY DIFFRACTION98.87
1.65-1.890.19561840.1543036X-RAY DIFFRACTION99.97
1.89-2.380.20081310.19323067X-RAY DIFFRACTION99.53
2.38-34.110.18831660.18223073X-RAY DIFFRACTION99.39
Refinement TLS params.Method: refined / Origin x: 15.9911568028 Å / Origin y: -0.72519814322 Å / Origin z: 5.71831103013 Å
111213212223313233
T0.0652726578732 Å20.0238422377528 Å20.0206673906957 Å2-0.0871246258445 Å20.00275657647383 Å2--0.0758093923765 Å2
L1.07197611391 °20.647122309308 °2-0.0509578336691 °2-1.58636555323 °2-0.192945441538 °2--1.39458235509 °2
S0.0325040574733 Å °0.054692613886 Å °0.125274740927 Å °0.145821917588 Å °0.0331880602199 Å °0.245323848924 Å °-0.00311130107025 Å °-0.0934527993044 Å °-0.0541963943655 Å °
Refinement TLS groupSelection details: chain 'A'

+
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