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- PDB-1hg5: CALM-N N-terminal domain of clathrin assembly lymphoid myeloid le... -

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Basic information

Entry
Database: PDB / ID: 1hg5
TitleCALM-N N-terminal domain of clathrin assembly lymphoid myeloid leukaemia protein, inositol(1,2,3,4,5,6)P6 complex
ComponentsCLATHRIN ASSEMBLY PROTEIN SHORT FORM
KeywordsENDOCYTOSIS / ADAPTOR
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
INOSITOL HEXAKISPHOSPHATE / Phosphatidylinositol-binding clathrin assembly protein / Phosphatidylinositol-binding clathrin assembly protein
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionDec 12, 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 1.3Oct 7, 2020Group: Other / Structure summary / Category: chem_comp / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLATHRIN ASSEMBLY PROTEIN SHORT FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5262
Polymers32,8661
Non-polymers6601
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.446, 77.446, 122.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 32865.789 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN RESIDUES 1-289
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: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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 CRYSTALS SOAKED IN 1MM LIGAND FOR 1 HOUR
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

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 CCD / Detector: CCD / Date: Mar 3, 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→41 Å / Num. obs: 25874 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 7 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.952 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.00952

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HF8

1hf8


Resolution: 2→65.94 Å / SU B: 6.90327 / SU ML: 0.18632 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14963 / ESU R Free: 0.13444
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SCALING DETAILS BABINET"S PRINCIPLE FOR SCALING HAS BEEN USED BULK SOLVENT CORRECTION BASED ON CONSTANT VALUE HAS BEEN U PARAMETERS FOR MASK ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SCALING DETAILS BABINET"S PRINCIPLE FOR SCALING HAS BEEN USED BULK SOLVENT CORRECTION BASED ON CONSTANT VALUE HAS BEEN U PARAMETERS FOR MASK CALCULATION VDW PROB RADII = 1.40 ION PROB RADII = 0.80 SHRINKAGE RADII = 0.80
RfactorNum. reflection% reflectionSelection details
Rfree0.21723 1310 5.1 %RANDOM
Rwork0.19159 ---
obs0.19286 24505 97.8 %-
Displacement parametersBiso mean: 44.384 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2--1.55 Å20 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 36 129 2279
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0370.022
X-RAY DIFFRACTIONp_angle_d2.461.95
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.61.5
X-RAY DIFFRACTIONp_mcangle_it2.92
X-RAY DIFFRACTIONp_scbond_it4.23
X-RAY DIFFRACTIONp_scangle_it6.64.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.160.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19286 / Rfactor Rfree: 0.21723 / Rfactor Rwork: 0.19159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.384 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.031
X-RAY DIFFRACTIONp_angle_d2.4

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