[English] 日本語
Yorodumi
- PDB-7jxv: ANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jxv
TitleANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia protein) bound to ubiquitin
Components
  • Phosphatidylinositol-binding clathrin assembly protein
  • Ubiquitin
KeywordsENDOCYTOSIS / Complex
Function / homology
Function and homology information


RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / regulation of terminal button organization / 1-phosphatidylinositol binding / positive regulation of synaptic vesicle clustering / amyloid-beta clearance by transcytosis / extrinsic component of presynaptic endocytic zone membrane / regulation of protein transport ...RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / regulation of terminal button organization / 1-phosphatidylinositol binding / positive regulation of synaptic vesicle clustering / amyloid-beta clearance by transcytosis / extrinsic component of presynaptic endocytic zone membrane / regulation of protein transport / positive regulation of amyloid precursor protein catabolic process / synaptic vesicle maturation / clathrin coat of coated pit / clathrin heavy chain binding / regulation of vesicle size / regulation of synaptic vesicle transport / postsynaptic endocytic zone / Golgi Associated Vesicle Biogenesis / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / positive regulation of dendrite extension / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / positive regulation of axonogenesis / positive regulation of Ras protein signal transduction / regulation of amyloid precursor protein catabolic process / clathrin-coated vesicle / endosomal transport / neurofibrillary tangle / low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta formation / clathrin binding / dendrite morphogenesis / parallel fiber to Purkinje cell synapse / regulation of endocytosis / hemopoiesis / synaptic vesicle endocytosis / regulation of synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / clathrin-coated pit / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / receptor-mediated endocytosis / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / axonogenesis / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / SNARE binding / Translesion synthesis by POLI
Similarity search - Function
ANTH domain superfamily / Clathrin coat assembly protein AP180-like / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / ENTH/VHS / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : ...ANTH domain superfamily / Clathrin coat assembly protein AP180-like / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / ENTH/VHS / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol-binding clathrin assembly protein / Polyubiquitin-C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsPashkova, N. / Gakhar, L. / Schnicker, N.J. / Piper, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM058202 United States
CitationJournal: Elife / Year: 2021
Title: ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals.
Authors: Pashkova, N. / Gakhar, L. / Yu, L. / Schnicker, N.J. / Minard, A.Y. / Winistorfer, S. / Johnson, I.E. / Piper, R.C.
History
DepositionAug 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol-binding clathrin assembly protein
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)41,8982
Polymers41,8982
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, NMR titration confirmed 1:1 ratio
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.068, 94.068, 91.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

-
Components

#1: Protein Phosphatidylinositol-binding clathrin assembly protein / Clathrin assembly lymphoid myeloid leukemia protein / rCALM


Mass: 33321.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Picalm, Calm / Production host: Escherichia coli (E. coli) / References: UniProt: O55012
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6, 0.2 M NaCl, 20% w/v MPEG2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→18.83 Å / Num. obs: 17581 / % possible obs: 99.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 40.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.027 / Rrim(I) all: 0.1 / Net I/σ(I): 22.1 / Num. measured all: 238917 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.4413.90.942433317490.9180.260.9753.296.5
8.79-18.838.50.03930493600.9990.0130.04250.290

-
Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.15data scaling
PHASERphasing
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 3ZYK

1ubq

3zyk


Resolution: 2.35→18.83 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 870 4.99 %
Rwork0.2062 16562 -
obs0.2093 17432 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.93 Å2
Refinement stepCycle: LAST / Resolution: 2.35→18.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 0 97 2836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01372791
X-RAY DIFFRACTIONf_angle_d1.6333761
X-RAY DIFFRACTIONf_chiral_restr0.0708433
X-RAY DIFFRACTIONf_plane_restr0.0089481
X-RAY DIFFRACTIONf_dihedral_angle_d19.15131060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.50.36851180.25072677X-RAY DIFFRACTION97.83
2.5-2.690.33431100.26582782X-RAY DIFFRACTION100
2.69-2.960.34821790.25522703X-RAY DIFFRACTION99.97
2.96-3.390.33241400.24922771X-RAY DIFFRACTION99.9
3.39-4.260.26071610.1912734X-RAY DIFFRACTION98.07
4.26-18.830.18531620.15942895X-RAY DIFFRACTION98.68

+
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