[English] 日本語
Yorodumi
- SASDCS6: Rap guanine nucleotide exchange factor 3 (isoform3) bound to RAS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDCS6
SampleRap guanine nucleotide exchange factor 3 (isoform3) bound to RAS related protein 1b - with cAMP
  • Rap guanine nucleotide exchange factor 3 (protein), EPAC1B, Homo sapiens
  • RAS related protein 1b (protein), Rap1b, Mus musculus
Function / homology
Function and homology information


Rap protein signal transduction / regulation of cell junction assembly / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / establishment of endothelial barrier / regulation of establishment of cell polarity / lipid droplet / cellular response to cAMP / small monomeric GTPase / GDP binding ...Rap protein signal transduction / regulation of cell junction assembly / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / establishment of endothelial barrier / regulation of establishment of cell polarity / lipid droplet / cellular response to cAMP / small monomeric GTPase / GDP binding / cell-cell junction / GTPase activity / GTP binding / protein-containing complex binding / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rap1 / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family ...Ras-related protein Rap1 / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Isoform 3 of Rap guanine nucleotide exchange factor 3 / :
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1144
Type: atomic / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Comment: Combined remodelled 3CF6 with 4F7Z and SwissModel / Chi-square value: 0.81 / P-value: 0.022800
Search similar-shape structures of this assembly by Omokage search (details)
Model #1145
Type: dummy / Radius of dummy atoms: 3.75 A / Symmetry: P1 / Comment: SAXNS_DAMMIF / Chi-square value: 0.588289 / P-value: 0.008000
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Rap guanine nucleotide exchange factor 3 (isoform3) bound to RAS related protein 1b - with cAMP
Specimen concentration: 1.00-4.00 / Entity id: 595 / 596
BufferName: 1mM EDTA, 10mM DTT, 500mM NaCl, 1mM cAMP, and 10mM Tris
pH: 9
Entity #595Name: EPAC1B / Type: protein / Description: Rap guanine nucleotide exchange factor 3 / Formula weight: 100.001 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: O95398-3
Sequence: GSPGIRVLVL RRMHRPRSCS YQLLLEHQRP SCIQGLRWTP LTNSEESLDF SESLEQASTE RVLRAGRQLH RHLLATCPNL IRDRKYHLRL YRQCCSGREL VDGILALGLG VHSRSQVVGI CQVLLDEGAL CHVKHDWAFQ DRDAQFYRFP GPEPEPVGTH EMEEELAEAV ...Sequence:
GSPGIRVLVL RRMHRPRSCS YQLLLEHQRP SCIQGLRWTP LTNSEESLDF SESLEQASTE RVLRAGRQLH RHLLATCPNL IRDRKYHLRL YRQCCSGREL VDGILALGLG VHSRSQVVGI CQVLLDEGAL CHVKHDWAFQ DRDAQFYRFP GPEPEPVGTH EMEEELAEAV ALLSQRGPDA LLTVALRKPP GQRTDEELDL IFEELLHIKA VAHLSNSVKR ELAAVLLFEP HSKAGTVLFS QGDKGTSWYI IWKGSVNVVT HGKGLVTTLH EGDDFGQLAL VNDAPRAATI ILREDNCHFL RVDKQDFNRI IKDVEAKTMR LEEHGKVVLV LERASQGAGP SRPPTPGRNR YTVMSGTPEK ILELLLEAMG PDSSAHDPTE TFLSDFLLTH RVFMPSAQLC AALLHHFHVE PAGGSEQERS TYVCNKRQQI LRLVSQWVAL YGSMLHTDPV ATSFLQKLSD LVGRDTRLSN LLREQWPERR RCHRLENGCG NASPQMKARN LPVWLPNQDE PLPGSSCAIQ VGDKVPYDIC RPDHSVLTLQ LPVTASVREV MAALAQEDGW TKGQVLVKVN SAGDAIGLQP DARGVATSLG LNERLFVVNP QEVHELIPHP DQLGPTVGSA EGLDLVSAKD LAGQLTDHDW SLFNSIHQVE LIHYVLGPQH LRDVTTANLE RFMRRFNELQ YWVATELCLC PVPGPRAQLL RKFIKLAAHL KEQKNLNSFF AVMFGLSNSA ISRLAHTWER LPHKVRKLYS ALERLLDPSW NHRVYRLALA KLSPPVIPFM PLLLKDMTFI HEGNHTLVEN LINFEKMRMM ARAARMLHHC RSHNPVPLSP LRSRVSHLHE DSQVARISTC SEQSLSTRSP ASTWAYVQQL KVIDNQRELS RLSRELEP
Entity #596Name: Rap1b / Type: protein / Description: RAS related protein 1b / Formula weight: 18 / Num. of mol.: 1 / Source: Mus musculus / References: UniProt: q52l50
Sequence:
MREYKLVVLG SGGVGKSALT VQFVQGIFVE KYDPTIEDSY RKQVEVDAQQ CMLEILDTAG TEQFTAMRDL YMKNGQGFAL VYSITAQSTF NDLQDLREQI LRVKDTDDVP MILVGNKCDL EDERVVGKEQ GQNLARQWNN CAFLESSAKS KINVNEIFYD LVRQINR

-
Experimental information

BeamInstrument name: Sealy Center For Structural Biology, UTMB-G Rigaku BioSAXS-1000
City: Galveston, TX / 国: USA / Type of source: X-ray in house / Wavelength: 0.15418 Å / Dist. spec. to detc.: 0.489 mm
DetectorName: Rigaku BioSAXS-1000 / Type: Kratky-2D / Pixsize x: 0.001 mm
Scan
Title: Rap guanine nucleotide exchange factor 3 (isoform3) bound to RAS related protein 1b - with cAMP
Measurement date: Apr 1, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1800 sec. / Number of frames: 5 / Unit: 1/A /
MinMax
Q0.0123 0.6788
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 129 /
MinMax
Q0.0137 0.1964
P(R) point2 130
R0 141.7
Result
Type of curve: single_conc /
ExperimentalPorod
MW119 kDa124 kDa
Volume-207 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I087670 763 85780 1523
Radius of gyration, Rg4.27 nm0.03 4.05 nm0.09

MinMax
D-14.2
Guinier point2 14

+
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