[English] 日本語
Yorodumi
- PDB-1e42: Beta2-adaptin appendage domain, from clathrin adaptor AP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1.0E+42
TitleBeta2-adaptin appendage domain, from clathrin adaptor AP2
ComponentsAP-2 COMPLEX SUBUNIT BETA
KeywordsENDOCYTOSIS / ADAPTOR
Function / homology
Function and homology information


Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance ...Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance / clathrin-dependent endocytosis / coronary vasculature development / signal sequence binding / endolysosome membrane / Nef Mediated CD4 Down-regulation / aorta development / ventricular septum development / clathrin binding / Recycling pathway of L1 / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / kidney development / intracellular protein transport / clathrin-coated endocytic vesicle membrane / cytoplasmic side of plasma membrane / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / postsynapse / Potential therapeutics for SARS / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain ...Immunoglobulin-like - #1150 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TATA-Binding Protein / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DITHIANE DIOL / NICKEL (II) ION / AP-2 complex subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsOwen, D.J. / Evans, P.R. / McMahon, H.T.
CitationJournal: Embo J. / Year: 2000
Title: The Structure and Function of the Beta2-Adaptin Appendage Domain
Authors: Owen, D.J. / Vallis, Y. / Pearse, B.M.F. / Mcmahon, H.T. / Evans, P.R.
History
DepositionJun 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: AP-2 COMPLEX SUBUNIT BETA
B: AP-2 COMPLEX SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,96315
Polymers58,1772
Non-polymers78613
Water14,808822
1
A: AP-2 COMPLEX SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4286
Polymers29,0881
Non-polymers3405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AP-2 COMPLEX SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5359
Polymers29,0881
Non-polymers4478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.040, 124.590, 67.640
Angle α, β, γ (deg.)90.00, 124.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.379985, 0.020033, -0.924776), (-0.011062, -0.999792, -0.017113), (-0.924927, 0.003727, 0.380127)
Vector: 4.137, 50.052, -5.467)
DetailsTHE BETA-ADAPTIN PROTEIN IS PART OF THE ASSEMBLY PROTEINCOMPLEX 2, (AP-2), THAT IS A HETEROTETRAMER COMPOSED OF TWO LARGE CHAINS (ALPHA AND BETA), A MEDIUM CHAIN (AP50)AND A SMALL CHAIN (AP17).

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein AP-2 COMPLEX SUBUNIT BETA / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA ...PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B / BETA2-ADAPTIN / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA SUBUNIT / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT BETA


Mass: 29088.453 Da / Num. of mol.: 2 / Fragment: APPENDAGE DOMAIN, RESIDUES 701-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P63010

-
Non-polymers , 6 types, 835 molecules

#2: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsCLONING HEADER MGSSHHHHHHSSGLVPRGSHM THEN RESIDUE 701-937

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 55 %
Crystal growpH: 8.8
Details: WELL SOLUTION: 1.6 - 2.0M MGCL2, 0.1M BICINE PH 8.7 - 9.0, 15% GLYCEROL, 1MM DTT. PROTEIN: 40MG/ML, 5MM HEPES, 50MM NACL, 4MM DTT, 1:1 MIXTURE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 8.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mMHEPES1drop
250 mM1dropNaCl
34 mMdithiothreitol1drop
440 mg/mlprotein1drop
51.6-2.0 M1reservoirMgCl2
60.1 MBicine1reservoirpH8.7-9.0
715 %(v/v)glycerol1reservoir
810 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 15, 1998
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.7→19.96 Å / Num. obs: 71562 / % possible obs: 98.4 % / Observed criterion σ(I): 4 / Redundancy: 6.85 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 11.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.48 / Rsym value: 0.75 / % possible all: 89.6
Reflection shell
*PLUS
% possible obs: 98.3 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→67.42 Å / SU B: 3.538 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.164
Details: RESIDUES A980 AND B980 WERE MODELLED AS GLYCEROL, BUT IDENTIFICATION IS NOT CERTAIN. RESIDUE B970 WAS MODELLED AS A 50% NI ION, SINCE IT IS BOUND TO A HISTIDINE, BUT IT MAY BE ANOTHER MG ION
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3621 5.057 %RANDOM
Rwork0.196 ---
obs-67980 98.3 %-
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20.8 Å2
2---2.4 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 37 822 4555
Software
*PLUS
Name: REFMAC / Version: VERSION 5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_deg1.9

+
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