[English] 日本語
Yorodumi
- PDB-6qiy: CI-2, conformation 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qiy
TitleCI-2, conformation 1
ComponentsSubtilisin-chymotrypsin inhibitor-2A
KeywordsPLANT PROTEIN / CHYMOTRYPSIN INHIBITOR 2 / protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / response to wounding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRomero, A. / Ruiz, F.M.
CitationJournal: Nat Commun / Year: 2019
Title: Engineering protein assemblies with allosteric control via monomer fold-switching.
Authors: Luis A Campos / Rajendra Sharma / Sara Alvira / Federico M Ruiz / Beatriz Ibarra-Molero / Mourad Sadqi / Carlos Alfonso / Germán Rivas / Jose M Sanchez-Ruiz / Antonio Romero Garrido / José ...Authors: Luis A Campos / Rajendra Sharma / Sara Alvira / Federico M Ruiz / Beatriz Ibarra-Molero / Mourad Sadqi / Carlos Alfonso / Germán Rivas / Jose M Sanchez-Ruiz / Antonio Romero Garrido / José M Valpuesta / Victor Muñoz /
Abstract: The macromolecular machines of life use allosteric control to self-assemble, dissociate and change shape in response to signals. Despite enormous interest, the design of nanoscale allosteric ...The macromolecular machines of life use allosteric control to self-assemble, dissociate and change shape in response to signals. Despite enormous interest, the design of nanoscale allosteric assemblies has proven tremendously challenging. Here we present a proof of concept of allosteric assembly in which an engineered fold switch on the protein monomer triggers or blocks assembly. Our design is based on the hyper-stable, naturally monomeric protein CI2, a paradigm of simple two-state folding, and the toroidal arrangement with 6-fold symmetry that it only adopts in crystalline form. We engineer CI2 to enable a switch between the native and an alternate, latent fold that self-assembles onto hexagonal toroidal particles by exposing a favorable inter-monomer interface. The assembly is controlled on demand via the competing effects of temperature and a designed short peptide. These findings unveil a remarkable potential for structural metamorphosis in proteins and demonstrate key principles for engineering protein-based nanomachinery.
History
DepositionJan 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subtilisin-chymotrypsin inhibitor-2A


Theoretical massNumber of molelcules
Total (without water)7,4121
Polymers7,4121
Non-polymers00
Water1,17165
1
A: Subtilisin-chymotrypsin inhibitor-2A
x 12


Theoretical massNumber of molelcules
Total (without water)88,94012
Polymers88,94012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation10_555-y,-x,-z1
crystal symmetry operation11_555-x+y,y,-z1
crystal symmetry operation12_555x,x-y,-z1
Buried area19520 Å2
ΔGint-95 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.773, 68.773, 50.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-144-

HOH

-
Components

#1: Protein Subtilisin-chymotrypsin inhibitor-2A / CI-2A


Mass: 7411.657 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli (E. coli) / References: UniProt: P01053
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.4 M AMMONIUM SULPHATE AND 100 MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→38.55 Å / Num. obs: 11793 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.02 / Net I/σ(I): 23
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIX(1.10_2155: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CI2

2ci2


Resolution: 1.5→38.55 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.6
RfactorNum. reflection% reflection
Rfree0.257 578 4.92 %
Rwork0.211 --
obs0.213 11750 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms521 0 0 65 586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006535
X-RAY DIFFRACTIONf_angle_d0.863727
X-RAY DIFFRACTIONf_dihedral_angle_d17.627339
X-RAY DIFFRACTIONf_chiral_restr0.0688
X-RAY DIFFRACTIONf_plane_restr0.00693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.65110.35011410.32062704X-RAY DIFFRACTION99
1.6511-1.890.26411360.24422741X-RAY DIFFRACTION100
1.89-2.38110.24931480.24082771X-RAY DIFFRACTION99
2.3811-38.5590.25021530.18822956X-RAY DIFFRACTION100
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)
15.48630.35430.51398.08250.31662.4338-0.0962-0.08610.3170.1217-0.2157-0.8611-0.16280.16150.3230.22120.0163-0.03990.24720.03520.284821.807916.316214.1938
22.4341.1246-1.46485.03020.75841.3438-0.04380.55990.1535-0.8291-0.09030.8349-0.1472-0.25750.04990.35670.03-0.12340.32810.03350.45259.724118.20758.5052
33.7201-1.60050.56687.56310.32232.65990.02420.0566-0.1926-0.2435-0.01920.34110.2-0.16480.010.18370.00470.00540.19540.00390.238314.594810.427611.6179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 25 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 26 THROUGH 47 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 48 THROUGH 66 )

+
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