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- PDB-3zyk: Structure of CALM (PICALM) ANTH domain -

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Basic information

Entry
Database: PDB / ID: 3zyk
TitleStructure of CALM (PICALM) ANTH domain
ComponentsPHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN
KeywordsENDOCYTOSIS / ENDOBREVIN / SYNAPTOBREVIN / VAMP2 / VAMP3 / AP180 / PLASMA MEMBRANE / ADAPTOR PROTEIN
Function / homology
Function and homology information


regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process / membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / synaptic vesicle budding from presynaptic endocytic zone membrane / 1-phosphatidylinositol binding / regulation of terminal button organization / positive regulation of synaptic vesicle clustering ...regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process / membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / 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 / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / regulation of synaptic vesicle transport / Golgi Associated Vesicle Biogenesis / amyloid-beta clearance by transcytosis / clathrin heavy chain binding / clathrin coat of coated pit / regulation of vesicle size / synaptic vesicle maturation / negative regulation of receptor-mediated endocytosis / negative regulation of protein localization to cell surface / 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 / negative regulation of protein localization to plasma membrane / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / neurofibrillary tangle / clathrin-coated vesicle / regulation of synaptic vesicle endocytosis / endosomal transport / low-density lipoprotein particle receptor binding / clathrin binding / positive regulation of axonogenesis / positive regulation of amyloid-beta formation / hemopoiesis / regulation of endocytosis / synaptic vesicle endocytosis / clathrin-coated pit / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / axonogenesis / receptor-mediated endocytosis / SNARE binding / Schaffer collateral - CA1 synapse / tau protein binding / receptor internalization / small GTPase binding / SH3 domain binding / multicellular organismal-level iron ion homeostasis / endocytosis / regulation of protein localization / synaptic vesicle / presynaptic membrane / postsynapse / postsynaptic membrane / intracellular iron ion homeostasis / vesicle / 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 / membrane / identical protein binding / 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
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMiller, S.E. / Sahlender, D.A. / Graham, S.C. / Honing, S. / Robinson, M.S. / Peden, A.A. / Owen, D.J.
CitationJournal: Cell / Year: 2011
Title: The molecular basis for the endocytosis of small R-SNAREs by the clathrin adaptor CALM.
Authors: Miller, S.E. / Sahlender, D.A. / Graham, S.C. / Honing, S. / Robinson, M.S. / Peden, A.A. / Owen, D.J.
History
DepositionAug 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN
B: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,0572
Polymers67,0572
Non-polymers00
Water7,476415
1
A: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,5291
Polymers33,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,5291
Polymers33,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.541, 78.313, 120.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND NOT (RESI 44 OR RESI 47:48 OR...
211CHAIN B
112CHAIN A AND RESI 271:288
212CHAIN B

NCS ensembles :
ID
1
2

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Components

#1: Protein PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN / CALM / CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN / RCALM


Mass: 33528.551 Da / Num. of mol.: 2 / Fragment: ANTH DOMAIN, RESIDUES 1-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX 4T2 CALMANTH(1-289) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: O55012
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GSPIGIH SEQUENCE IS RESIDUAL FROM AFFINITY TAG AND CLONING.

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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: 2.58 Å3/Da / Density % sol: 52.35 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING EQUAL AMOUNTS (200-400 NL) OF PROTEIN (15 MG/ML IN 20 MM HEPES PH 7.4, 120 MM NACL, 4 MM DTT) AND RESERVOIR SOLUTION (100 MM BIS TRIS PROPANE, ...Details: CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING EQUAL AMOUNTS (200-400 NL) OF PROTEIN (15 MG/ML IN 20 MM HEPES PH 7.4, 120 MM NACL, 4 MM DTT) AND RESERVOIR SOLUTION (100 MM BIS TRIS PROPANE, 200 MM SODIUM MALONATE, 20% (W/V) PEG 3350) AND EQUILIBRATED AGAINST 80 UL OF RESERVOIR SOLUTION AT 16C. CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION (5-60 S) IN RESERVOIR SOLUTION SUPPLEMENTED WITH 25% GLYCEROL AND WERE RAPIDLY CRYOCOOLED IN LIQUID N2 OR A 100 K STREAM OF N2 GAS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→73.5 Å / Num. obs: 64198 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HF8

1hf8


Resolution: 1.8→40.009 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 3237 5.1 %
Rwork0.1816 --
obs0.1833 64141 98.62 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.677 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 35.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.4595 Å20 Å20 Å2
2--1.8671 Å20 Å2
3----5.3266 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 0 415 4722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094510
X-RAY DIFFRACTIONf_angle_d1.0776104
X-RAY DIFFRACTIONf_dihedral_angle_d12.451740
X-RAY DIFFRACTIONf_chiral_restr0.075695
X-RAY DIFFRACTIONf_plane_restr0.005782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1929X-RAY DIFFRACTIONPOSITIONAL
12B1929X-RAY DIFFRACTIONPOSITIONAL0.075
21A111X-RAY DIFFRACTIONPOSITIONAL
22B111X-RAY DIFFRACTIONPOSITIONAL0.024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82690.34721150.30132629X-RAY DIFFRACTION98
1.8269-1.85540.33311470.26552579X-RAY DIFFRACTION98
1.8554-1.88580.26671540.25362600X-RAY DIFFRACTION98
1.8858-1.91830.27051270.21222605X-RAY DIFFRACTION98
1.9183-1.95320.25441390.19892597X-RAY DIFFRACTION98
1.9532-1.99080.2391370.19312624X-RAY DIFFRACTION98
1.9908-2.03140.24511350.1842590X-RAY DIFFRACTION98
2.0314-2.07560.21721440.18872601X-RAY DIFFRACTION98
2.0756-2.12390.22441390.17942631X-RAY DIFFRACTION99
2.1239-2.1770.23881560.17962622X-RAY DIFFRACTION99
2.177-2.23580.21161480.17642630X-RAY DIFFRACTION99
2.2358-2.30160.21091320.17132621X-RAY DIFFRACTION99
2.3016-2.37590.2131340.17512637X-RAY DIFFRACTION99
2.3759-2.46080.20491520.17282635X-RAY DIFFRACTION99
2.4608-2.55930.16711540.17182649X-RAY DIFFRACTION99
2.5593-2.67580.21381580.17832615X-RAY DIFFRACTION99
2.6758-2.81680.20951330.17812700X-RAY DIFFRACTION99
2.8168-2.99320.22751340.18282677X-RAY DIFFRACTION99
2.9932-3.22430.23071430.19062670X-RAY DIFFRACTION99
3.2243-3.54860.1881360.17792710X-RAY DIFFRACTION99
3.5486-4.06160.20751460.16132711X-RAY DIFFRACTION100
4.0616-5.11550.20981330.15712718X-RAY DIFFRACTION98
5.1155-40.01840.20341410.20182853X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4246-0.38560.11430.9338-0.3481.33940.01720.03710.0245-0.043-0.00210.0208-0.072-0.19170.00050.04050.0064-0.00020.0651-0.00790.0699-29.2251-1.31040.453
20.7357-0.07720.51141.40.08653.94790.0271-0.03810.03730.1985-0.0224-0.19110.33930.59420.00810.0940.0001-0.04130.16160.02720.1099-18.2652-11.454730.3847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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