[English] 日本語
Yorodumi
- PDB-4ofp: Crystal Structure of SYG-2 D3-D4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ofp
TitleCrystal Structure of SYG-2 D3-D4
ComponentsProtein SYG-2
KeywordsCELL ADHESION / Immunoglobulin superfamily / Synaptogenesis / Protein Binding / N-linked Glycosylation / Membrane / Extracellular / SIGNALING PROTEIN
Function / homology
Function and homology information


Nephrin family interactions / synaptic target recognition / protein complex involved in cell adhesion / collateral sprouting / protein localization to synapse / synapse assembly / cell adhesion molecule binding / synaptic membrane / synapse organization / cell-cell adhesion ...Nephrin family interactions / synaptic target recognition / protein complex involved in cell adhesion / collateral sprouting / protein localization to synapse / synapse assembly / cell adhesion molecule binding / synaptic membrane / synapse organization / cell-cell adhesion / cell-cell junction / cell-cell signaling / protein homodimerization activity / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptogenesis protein syg-2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOzkan, E. / Garcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Extracellular Architecture of the SYG-1/SYG-2 Adhesion Complex Instructs Synaptogenesis.
Authors: Ozkan, E. / Chia, P.H. / Wang, R.R. / Goriatcheva, N. / Borek, D. / Otwinowski, Z. / Walz, T. / Shen, K. / Garcia, K.C.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein SYG-2
B: Protein SYG-2
C: Protein SYG-2
D: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,16510
Polymers91,8384
Non-polymers1,3276
Water0
1
A: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6234
Polymers22,9591
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein SYG-2


Theoretical massNumber of molelcules
Total (without water)22,9591
Polymers22,9591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1812
Polymers22,9591
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein SYG-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4023
Polymers22,9591
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.240, 121.240, 178.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
Protein SYG-2


Mass: 22959.475 Da / Num. of mol.: 4 / Fragment: D3-D4, UNP residues 231-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C26G2.1, CELE_C26G2.1, syg-2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q9U3P2
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.9 M Diammonium tartrate, 0.1 M Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2012
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 27368 / Num. obs: 27351 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.4 % / Biso Wilson estimate: 106.06 Å2 / Rsym value: 0.158 / Net I/σ(I): 13.15

-
Processing

Software
NameVersionClassification
Blu-Ice(modified)data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1492)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4OFK

4ofk


Resolution: 3→46.315 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 30.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 1365 5 %Random
Rwork0.2418 ---
all0.2439 27291 --
obs0.2439 27288 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5948 0 84 0 6032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066167
X-RAY DIFFRACTIONf_angle_d1.0558393
X-RAY DIFFRACTIONf_dihedral_angle_d10.5692273
X-RAY DIFFRACTIONf_chiral_restr0.045967
X-RAY DIFFRACTIONf_plane_restr0.0061110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.36541340.32212543X-RAY DIFFRACTION100
3.1072-3.23160.35651330.30932532X-RAY DIFFRACTION100
3.2316-3.37860.34231350.29192564X-RAY DIFFRACTION100
3.3786-3.55670.31621330.27082538X-RAY DIFFRACTION100
3.5567-3.77940.32351360.26412566X-RAY DIFFRACTION100
3.7794-4.07110.29971350.24472576X-RAY DIFFRACTION100
4.0711-4.48050.24911350.20752573X-RAY DIFFRACTION100
4.4805-5.12810.23491380.19762604X-RAY DIFFRACTION100
5.1281-6.4580.28351380.2512636X-RAY DIFFRACTION100
6.458-46.32090.27881480.24022791X-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)
11.1529-1.2247-0.51555.90773.09362.29750.1108-0.027-1.41880.88180.4891-1.31660.75160.82510.4457-0.02920.35920.53191.29420.35081.001712.14498.105741.5028
26.59080.6666-1.7392.69042.4063.6977-0.1235-0.17390.48530.90690.1667-0.0995-0.33730.0307-0.12470.77490.0914-0.11920.84430.13430.69944.215423.78256.8244
34.2101-2.13991.24384.0647-1.86834.21140.61280.7351.3631-0.8346-0.20840.2213-0.40160.1095-0.32770.7321-0.010.1571.65240.68561.51289.037537.488416.3897
41.98430.62540.16434.68560.43563.3607-0.40952.5550.9854-0.48750.71790.2337-1.1357-1.16210.76041.33880.485-0.05243.06941.27081.6797-10.194241.3723-6.413
50.2179-0.94960.84045.9961-2.67993.85950.94112.03250.7793-1.4647-0.8134-0.1611-1.137-0.76141.29481.53610.6277-0.15533.49091.86771.7236-9.196445.1105-5.032
60.5626-1.06620.84341.6592-1.73175.98010.18350.79311.50220.009-0.25070.1577-0.67420.1474-0.07210.58480.04820.00941.14810.72241.3994-13.251235.121424.8835
72.6778-1.49271.71221.708-0.49098.5246-0.01480.12980.386-0.10890.13780.64530.2376-0.0944-0.24240.4454-0.0391-0.0120.87060.4571.2985-12.806229.883733.9134
83.11231.54630.89594.429-1.29465.41540.40342.3659-0.5509-0.92690.19210.88151.6294-0.787-0.97251.29240.0454-0.21562.6952-0.081.4633-22.440417.6514-5.5245
9-0.0080.0350.02820.04150.02060.00970.57180.3522-1.3418-0.2424-0.1217-0.56691.0691-0.5269-0.13721.29320.126-0.71723.0892-0.06151.5545-12.08610.892-1.6321
103.5707-1.74371.69264.84741.46582.76880.94941.0486-0.2561-0.923-0.9457-0.56510.3179-0.21280.04730.95260.21310.12671.78970.50471.116517.452518.209414.5697
111.8174-0.4529-1.00313.81291.82213.80570.4651-0.0698-0.9276-0.40470.3373-1.63961.11420.8199-0.39651.05310.3833-0.04821.59240.12261.77617.10881.66732.9323
129.916-0.83691.73914.8965-0.3314.1662-0.09411.33020.6716-0.5742-0.3812-0.01760.44190.40880.50510.54930.10270.0910.91120.19160.548-18.969215.098420.7325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 230 through 259 )
2X-RAY DIFFRACTION2chain 'A' and (resid 260 through 321 )
3X-RAY DIFFRACTION3chain 'A' and (resid 322 through 429 )
4X-RAY DIFFRACTION4chain 'B' and (resid 234 through 281 )
5X-RAY DIFFRACTION5chain 'B' and (resid 282 through 311 )
6X-RAY DIFFRACTION6chain 'B' and (resid 312 through 374 )
7X-RAY DIFFRACTION7chain 'B' and (resid 375 through 430 )
8X-RAY DIFFRACTION8chain 'C' and (resid 234 through 296 )
9X-RAY DIFFRACTION9chain 'C' and (resid 297 through 334 )
10X-RAY DIFFRACTION10chain 'C' and (resid 335 through 429 )
11X-RAY DIFFRACTION11chain 'D' and (resid 230 through 321 )
12X-RAY DIFFRACTION12chain 'D' and (resid 322 through 429 )

+
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