[English] 日本語
Yorodumi
- PDB-3dow: Complex structure of GABA type A receptor associated protein and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dow
TitleComplex structure of GABA type A receptor associated protein and its binding epitope on calreticulin
Components
  • CRT peptide
  • Gamma-aminobutyric acid receptor-associated protein
KeywordsPROTEIN TRANSPORT / alpha-beta / beta-grasp fold / Cytoplasm / Cytoskeleton / Golgi apparatus / Membrane / Microtubule / Transport / Calcium / Chaperone / Endoplasmic reticulum / Extracellular matrix / Lectin / Metal-binding / Secreted / Zinc
Function / homology
Function and homology information


Calnexin/calreticulin cycle / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / positive regulation of protein K48-linked ubiquitination / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding ...Calnexin/calreticulin cycle / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / positive regulation of protein K48-linked ubiquitination / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus / intracellular glucocorticoid receptor signaling pathway / endoplasmic reticulum quality control compartment / sequestering of calcium ion / regulation of meiotic nuclear division / response to glycoside / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / hormone binding / regulation of Rac protein signal transduction / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / GABA receptor binding / cardiac muscle cell differentiation / molecular sequestering activity / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Scavenging by Class A Receptors / TBC/RABGAPs / microtubule associated complex / protein maturation by protein folding / Scavenging by Class F Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / Macroautophagy / beta-tubulin binding / response to testosterone / cellular response to lithium ion / axoneme / smooth endoplasmic reticulum / autophagosome membrane / autophagosome assembly / protein localization to nucleus / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of neuron differentiation / autophagosome / protein targeting / positive regulation of cell cycle / positive regulation of phagocytosis / : / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / endocytic vesicle lumen / sperm midpiece / protein export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell migration / acrosomal vesicle / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / intracellular calcium ion homeostasis / microtubule cytoskeleton organization / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / unfolded protein binding / cellular senescence / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / integrin binding / protein folding / response to estradiol / nuclear envelope / ER-Phagosome pathway / protein-folding chaperone binding / chemical synaptic transmission / cytoplasmic vesicle / microtubule binding / spermatogenesis / carbohydrate binding / collagen-containing extracellular matrix / regulation of apoptotic process / microtubule / negative regulation of translation / lysosome / protein stabilization / ribosome / response to xenobiotic stimulus / iron ion binding / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / mRNA binding / negative regulation of DNA-templated transcription
Similarity search - Function
Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like ...Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Endoplasmic reticulum targeting sequence. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Concanavalin A-like lectin/glucanase domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Calreticulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThielmann, Y. / Weiergraeber, O.H. / Willbold, D.
CitationJournal: Febs J. / Year: 2009
Title: Structural framework of the GABARAP-calreticulin interface - implications for substrate binding to endoplasmic reticulum chaperones.
Authors: Thielmann, Y. / Weiergraber, O.H. / Mohrluder, J. / Willbold, D.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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: Gamma-aminobutyric acid receptor-associated protein
B: CRT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4833
Polymers15,4182
Non-polymers651
Water52229
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5.7 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.043, 97.043, 97.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
DetailsThe predicted biological unit contains one copy of the monomeric GABARAP-CRT peptide complex.

-
Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 14086.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Product contains an N-terminal cloning artifact (glycine-serine) preceding the sequence of native GABARAP.
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O95166
#2: Protein/peptide CRT peptide / Calreticulin / CRP55 / Calregulin / HACBP / ERp60 / grp60


Mass: 1331.407 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide containing amino acids 195-205 of mature calreticulin, CALR_HUMAN, UniProt entry P27797
References: UniProt: P27797
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 27% v/v PEG MME 550, 10 mM ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2007 / Details: Mirrors
RadiationMonochromator: diamond, germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→39.62 Å / Num. all: 6892 / Num. obs: 6892 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.9 / Num. measured all: 6540 / Num. unique all: 985 / Rsym value: 0.399 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KJT

1kjt


Resolution: 2.3→34.31 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 327 -RANDOM
Rwork0.232 ---
all0.233 6892 --
obs0.233 6892 99.7 %-
Displacement parametersBiso max: 75.56 Å2 / Biso mean: 45.275 Å2 / Biso min: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 2 30 1067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_deg0.62
X-RAY DIFFRACTIONf_dihedral_angle_d16.5

+
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