[English] 日本語
Yorodumi
- PDB-4cbp: Crystal structure of neural ectodermal development factor IMP-L2. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cbp
TitleCrystal structure of neural ectodermal development factor IMP-L2.
ComponentsNEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2
KeywordsCELL ADHESION / IMAGINAL MORPHOGENESIS PROTEIN-LATE 2 / INSULIN BINDING / IMMUNOGLOBULIN DOMAIN / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


positive regulation of entry into reproductive diapause / response to insect / dendrite self-avoidance / cell-cell adhesion mediator activity / insulin binding / response to starvation / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of lipid storage / positive regulation of insulin receptor signaling pathway / negative regulation of insulin receptor signaling pathway ...positive regulation of entry into reproductive diapause / response to insect / dendrite self-avoidance / cell-cell adhesion mediator activity / insulin binding / response to starvation / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of lipid storage / positive regulation of insulin receptor signaling pathway / negative regulation of insulin receptor signaling pathway / axon guidance / determination of adult lifespan / axon / extracellular space / plasma membrane
Similarity search - Function
: / 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 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural/ectodermal development factor IMP-L2
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKulahin, N. / Kristensen, O. / Brzozowski, M. / Schluckebier, G. / Meyts, P.D.
CitationJournal: To be Published
Title: Structural Analysis of Imp-L2 Function
Authors: Kulahin, N. / Watson, C.J. / Turkenburg, J.P. / Kristensen, O. / Norrman, M. / Sajid, W. / Schluckebier, G. / Meyts, P.D. / Brzozowski, M.
History
DepositionOct 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.2May 29, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2
B: NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8354
Polymers60,6512
Non-polymers1842
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-5.4 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.856, 99.732, 56.280
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9872, -0.157, 0.0295), (-0.1518, 0.9794, 0.1329), (-0.0497, 0.1267, -0.9907)7.294, -10.722, 118.3484

-
Components

#1: Protein NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2 / NEURAL ECTODERMAL DEVELOPMENT FACTOR IMP-L2


Mass: 30325.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q09024
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: HANGING-DROP EXPERIMENTS BY MIXING 1 UL PROTEIN (5.5. MG/ML IN 10 MM HEPES PH 7.4, 20 MM NACL) AND 1 UL RESERVOIR SOLUTION (17% PEG-6000, 0.1 M TRIS HYDROCHLORIDE, PH 7.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.59→56.25 Å / Num. obs: 70546 / % possible obs: 95.7 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.4
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 71.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
MOSFLMdata reduction
xia2data scaling
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→29.542 Å / SU ML: 0.16 / σ(F): 1.91 / Phase error: 18.62 / Stereochemistry target values: ML / Details: REFINED AGAINST ANOMALOUS DATA
RfactorNum. reflection% reflection
Rfree0.1883 3844 2.8 %
Rwork0.1562 --
obs0.1571 69600 94.74 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→29.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 12 457 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063495
X-RAY DIFFRACTIONf_angle_d1.0864762
X-RAY DIFFRACTIONf_dihedral_angle_d11.7821321
X-RAY DIFFRACTIONf_chiral_restr0.04535
X-RAY DIFFRACTIONf_plane_restr0.004621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62910.2821330.23694669X-RAY DIFFRACTION65
1.6291-1.66040.26381700.21995512X-RAY DIFFRACTION74
1.6604-1.69430.2451730.20645908X-RAY DIFFRACTION82
1.6943-1.73120.2182000.18556518X-RAY DIFFRACTION89
1.7312-1.77140.23151980.16836992X-RAY DIFFRACTION95
1.7714-1.81570.20192080.16217303X-RAY DIFFRACTION100
1.8157-1.86480.16782250.15077219X-RAY DIFFRACTION100
1.8648-1.91970.19242130.14027327X-RAY DIFFRACTION100
1.9197-1.98160.1652100.1337258X-RAY DIFFRACTION100
1.9816-2.05240.17762100.13157291X-RAY DIFFRACTION100
2.0524-2.13460.182100.13437284X-RAY DIFFRACTION100
2.1346-2.23170.15622000.13237351X-RAY DIFFRACTION100
2.2317-2.34930.19262070.1397335X-RAY DIFFRACTION100
2.3493-2.49640.1672200.15437290X-RAY DIFFRACTION100
2.4964-2.68910.22382110.15977316X-RAY DIFFRACTION100
2.6891-2.95950.20542160.16317320X-RAY DIFFRACTION100
2.9595-3.38720.18342040.15737286X-RAY DIFFRACTION100
3.3872-4.26540.16632160.15537304X-RAY DIFFRACTION100
4.2654-29.54740.19532200.16847113X-RAY DIFFRACTION97

+
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