[English] 日本語
Yorodumi
- PDB-1hf8: CALM-N N-terminal domain of clathrin assembly lymphoid myeloid le... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hf8
TitleCALM-N N-terminal domain of clathrin assembly lymphoid myeloid leukaemia protein
ComponentsCLATHRIN ASSEMBLY PROTEIN SHORT FORM
KeywordsCLATHRIN / TRISKELION / COATED VESICLES / ENDOCYTOSIS / SELF-ASSEMBLY / ALPHA-ALPHA SUPERHELIX
Function / homology
Function and homology information


RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / positive regulation of amyloid precursor protein catabolic process / postsynaptic endocytic zone / 1-phosphatidylinositol binding / synaptic vesicle budding from presynaptic endocytic zone membrane / regulation of terminal button organization / positive regulation of synaptic vesicle clustering ...RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / positive regulation of amyloid precursor protein catabolic process / postsynaptic endocytic zone / 1-phosphatidylinositol binding / synaptic vesicle budding from presynaptic endocytic zone membrane / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / regulation of protein transport / extrinsic component of presynaptic endocytic zone membrane / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle transport / amyloid-beta clearance by transcytosis / clathrin heavy chain binding / clathrin coat of coated pit / regulation of vesicle size / synaptic vesicle maturation / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / vesicle budding from membrane / positive regulation of dendrite extension / clathrin-dependent endocytosis / positive regulation of Ras protein signal transduction / regulation of amyloid precursor protein catabolic process / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / regulation of synaptic vesicle endocytosis / endosomal transport / neurofibrillary tangle / positive regulation of axonogenesis / positive regulation of amyloid-beta formation / clathrin binding / hemopoiesis / regulation of endocytosis / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / vesicle-mediated transport / axonogenesis / receptor-mediated endocytosis / SNARE binding / tau protein binding / Schaffer collateral - CA1 synapse / receptor internalization / SH3 domain binding / small GTPase binding / multicellular organismal-level iron ion homeostasis / endocytosis / synaptic vesicle / regulation of protein localization / presynaptic membrane / postsynaptic membrane / intracellular iron ion homeostasis / vesicle / postsynapse / postsynaptic density / early endosome / learning or memory / endosome / negative regulation of gene expression / neuronal cell body / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / cell surface / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
ANTH domain / Clathrin coat assembly protein AP180-like / ANTH domain superfamily / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS ...ANTH domain / Clathrin coat assembly protein AP180-like / ANTH domain superfamily / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol-binding clathrin assembly protein / Phosphatidylinositol-binding clathrin assembly protein
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsFord, M.G.J. / Evans, P.R. / McMahon, H.T.
CitationJournal: Science / Year: 2001
Title: Simultaneous Binding of Ptdins(4,5)P2 and Clathrin by Ap180 in the Nucleation of Clathrin Lattices on Membranes
Authors: Ford, M.G.J. / Pearse, B.M.F. / Higgins, M.K. / Vallis, Y. / Owen, D.J. / Gibson, A. / Hopkins, C.R. / Evans, P.R. / Mcmahon, H.T.
History
DepositionNov 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CLATHRIN ASSEMBLY PROTEIN SHORT FORM


Theoretical massNumber of molelcules
Total (without water)32,8661
Polymers32,8661
Non-polymers00
Water2,342130
1
A: CLATHRIN ASSEMBLY PROTEIN SHORT FORM

A: CLATHRIN ASSEMBLY PROTEIN SHORT FORM


Theoretical massNumber of molelcules
Total (without water)65,7322
Polymers65,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2220 Å2
ΔGint-6.6 kcal/mol
Surface area30440 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.929, 77.929, 121.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsBIOLOGICAL_UNIT: MONOMERTHIS DIMERIC ARRANGEMENT IS THE RESULT OF TIGHT CRYSTALPACKING.

-
Components

#1: Protein CLATHRIN ASSEMBLY PROTEIN SHORT FORM / AP180-2 / CALM-N


Mass: 32865.789 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX4T2 / Gene (production host): CALM-N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O55011, UniProt: O55012*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5 / Details: 0.1M HEPES, PH 7.5, 12% PEG 8K, 8% ETHYLENE GLYCOL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1reservoir
212-14 %PEG80001reservoir
38 %ethylene glycol1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 2, 2000
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→66 Å / Num. obs: 26116 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 14 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 27.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.036 / Mean I/σ(I) obs: 2.8 / Rsym value: 1.036 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→65.94 Å / SU B: 6.468 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1324 5.1 %RANDOM
Rwork0.19 ---
obs0.192 24733 98.7 %-
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 130 2244
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19207 / Rfactor Rfree: 0.22252 / Rfactor Rwork: 0.19049
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.199 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONp_bond_d0.0310.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.11.95
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.160.2
X-RAY DIFFRACTIONp_mcbond_it1.61.5
X-RAY DIFFRACTIONp_scbond_it4.23
X-RAY DIFFRACTIONp_mcangle_it2.92
X-RAY DIFFRACTIONp_scangle_it6.64.5

+
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