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- PDB-1hf8: CALM-N N-terminal domain of clathrin assembly lymphoid myeloid le... -

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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


membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / postsynaptic endocytic zone / positive regulation of amyloid precursor protein catabolic process / synaptic vesicle budding from presynaptic endocytic zone membrane / 1-phosphatidylinositol binding / regulation of terminal button organization / positive regulation of synaptic vesicle clustering ...membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / postsynaptic endocytic zone / positive regulation of amyloid precursor protein catabolic process / synaptic vesicle budding from presynaptic endocytic zone membrane / 1-phosphatidylinositol binding / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / regulation of protein transport / extrinsic component of presynaptic endocytic zone membrane / regulation of synaptic vesicle transport / Golgi Associated Vesicle Biogenesis / clathrin heavy chain binding / amyloid-beta clearance by transcytosis / 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 / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / vesicle budding from membrane / positive regulation of dendrite extension / clathrin-dependent endocytosis / regulation of amyloid precursor protein catabolic process / negative regulation of protein localization to plasma membrane / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / regulation of synaptic vesicle endocytosis / clathrin-coated vesicle / neurofibrillary tangle / endosomal transport / low-density lipoprotein particle receptor binding / clathrin binding / positive regulation of axonogenesis / positive regulation of amyloid-beta formation / regulation of endocytosis / hemopoiesis / synaptic vesicle endocytosis / clathrin-coated pit / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / receptor-mediated endocytosis / axonogenesis / SNARE binding / tau protein binding / Schaffer collateral - CA1 synapse / receptor internalization / small GTPase binding / multicellular organismal-level iron ion homeostasis / SH3 domain binding / endocytosis / regulation of protein localization / synaptic vesicle / presynaptic membrane / postsynaptic membrane / intracellular iron ion homeostasis / vesicle / postsynapse / postsynaptic density / learning or memory / early endosome / endosome / negative regulation of gene expression / neuronal cell body / positive regulation of DNA-templated transcription / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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.

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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

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Experimental details

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Experiment

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

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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
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 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 %

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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

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