[English] 日本語
Yorodumi
- PDB-8tkt: ZIG-4-INS-6 complex, C-centered monoclinic form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tkt
TitleZIG-4-INS-6 complex, C-centered monoclinic form
Components
  • Probable insulin-like peptide beta-type 5
  • Zwei Ig domain protein zig-4
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / NEUROPEPTIDE / SIGNALING PROTEIN / PROTEIN BINDING / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


negative regulation of dauer entry / dauer larval development / cellular response to salt / regulation of synaptic assembly at neuromuscular junction / chemosensory behavior / olfactory learning / neuron development / insulin receptor binding / hormone activity / insulin receptor signaling pathway ...negative regulation of dauer entry / dauer larval development / cellular response to salt / regulation of synaptic assembly at neuromuscular junction / chemosensory behavior / olfactory learning / neuron development / insulin receptor binding / hormone activity / insulin receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Nematode insulin-like peptide, beta type / : / Nematode insulin-related peptide beta type / : / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...Nematode insulin-like peptide, beta type / : / Nematode insulin-related peptide beta type / : / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Zwei Ig domain protein zig-4 / Probable insulin-like peptide beta-type 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCheng, S. / Baltrusaitis, E. / Aziz, Z. / Nawrocka, W.I. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 United States
CitationJournal: Biorxiv / Year: 2024
Title: Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways.
Authors: Nawrocka, W.I. / Cheng, S. / Hao, B. / Rosen, M.C. / Cortes, E. / Baltrusaitis, E.E. / Aziz, Z. / Kovacs, I.A. / Ozkan, E.
History
DepositionJul 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zwei Ig domain protein zig-4
B: Probable insulin-like peptide beta-type 5
C: Zwei Ig domain protein zig-4
D: Probable insulin-like peptide beta-type 5


Theoretical massNumber of molelcules
Total (without water)60,3744
Polymers60,3744
Non-polymers00
Water1267
1
A: Zwei Ig domain protein zig-4
B: Probable insulin-like peptide beta-type 5


Theoretical massNumber of molelcules
Total (without water)30,1872
Polymers30,1872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Zwei Ig domain protein zig-4
D: Probable insulin-like peptide beta-type 5


Theoretical massNumber of molelcules
Total (without water)30,1872
Polymers30,1872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.430, 56.654, 73.685
Angle α, β, γ (deg.)90.000, 113.247, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 43 through 136 or resid 138...
d_2ens_1(chain "C" and (resid 43 through 136 or resid 138...
d_1ens_2(chain "B" and (resid 63 or (resid 64 and (name...
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROHISHISAA43 - 1363 - 96
d_12ens_1THRTHRHISHISAA138 - 25098 - 210
d_21ens_1PROPROHISHISCC43 - 1363 - 96
d_22ens_1THRTHRHISHISCC138 - 25098 - 210
d_11ens_2GLYGLYPROPROBB63 - 1125 - 54
d_21ens_2GLYGLYPROPRODD63 - 1125 - 54

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.687748506915, -0.275613494988, 0.671594515029), (-0.194627830206, -0.961262079008, -0.195179976359), (0.699372575203, 0.00352375408172, -0.714748616096)-6.95293746865, -12.8546823602, 3.13309071759
2given(0.662627697418, -0.279219423044, 0.694953990139), (-0.206001300516, -0.960063900097, -0.189316591761), (0.720061107685, -0.0177150084854, -0.693684495772)-7.19900636346, -13.2434805574, 3.02484268385

-
Components

#1: Protein Zwei Ig domain protein zig-4


Mass: 23689.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zig-4 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5ECB1
#2: Protein Probable insulin-like peptide beta-type 5 / INS-6


Mass: 6497.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ins-6 / Cell (production host): Baculovirus / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P56174
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium/potassium phosphate, 0.1 M bis-tris propane, pH 6.8, 28% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→200 Å / Num. obs: 28028 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 56.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.131 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4412 / CC1/2: 0.652 / Rsym value: 1.131 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5015refinement
XDS20190806data reduction
XDS20190806data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→53.13 Å / SU ML: 0.3491 / Cross valid method: FREE R-VALUE / Phase error: 37.3522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1374 4.91 %Random selection
Rwork0.2152 26612 --
obs0.2172 27986 98.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→53.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 0 7 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263948
X-RAY DIFFRACTIONf_angle_d0.63115372
X-RAY DIFFRACTIONf_chiral_restr0.0446621
X-RAY DIFFRACTIONf_plane_restr0.0067701
X-RAY DIFFRACTIONf_dihedral_angle_d15.86391394
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.742136151496
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.06010811591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.47211330.43522584X-RAY DIFFRACTION95.27
2.38-2.470.45131310.38792630X-RAY DIFFRACTION98.89
2.47-2.590.41961250.33722683X-RAY DIFFRACTION99.08
2.59-2.720.36251190.31872660X-RAY DIFFRACTION99.04
2.72-2.890.30881420.28332630X-RAY DIFFRACTION98.58
2.89-3.120.33441310.24362693X-RAY DIFFRACTION99.44
3.12-3.430.27031420.22342656X-RAY DIFFRACTION99.36
3.43-3.930.21511440.19952674X-RAY DIFFRACTION98.6
3.93-4.950.19611330.16012688X-RAY DIFFRACTION98.12
4.95-53.130.21541740.17782714X-RAY DIFFRACTION98.16

+
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