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- PDB-3zyl: Structure of a truncated CALM (PICALM) ANTH domain -

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Basic information

Entry
Database: PDB / ID: 3zyl
TitleStructure of a truncated 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


membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / 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 ...membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / 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 / parallel fiber to Purkinje cell synapse / negative regulation of protein localization to plasma membrane / dendrite morphogenesis / regulation of synaptic vesicle endocytosis / clathrin-coated vesicle / neurofibrillary tangle / endosomal transport / low-density lipoprotein particle receptor binding / positive regulation of axonogenesis / clathrin binding / 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 / SNARE binding / receptor-mediated endocytosis / Schaffer collateral - CA1 synapse / tau protein binding / receptor internalization / small GTPase binding / multicellular organismal-level iron ion homeostasis / SH3 domain binding / 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 / 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
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)61,7912
Polymers61,7912
Non-polymers00
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-19 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.888, 121.082, 62.418
Angle α, β, γ (deg.)90.00, 110.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND NOT (RESID 28 OR RESID 65 OR RESID 111:115 OR RESID 186:190 OR RESID 237 OR RESID 252)
211CHAIN B

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Components

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


Mass: 30895.619 Da / Num. of mol.: 2 / Fragment: TRUNCATED ANTH DOMAIN, RESIDUES 1-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX 4T2 CALMANTH(1-264) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: O55012
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.74 Å3/Da / Density % sol: 55.14 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
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 (15% V/V ETHANOL, 100 MM ...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 (15% V/V ETHANOL, 100 MM IMIDAZOLE PH 8.0, 200 MM MGCL2) 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: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 20, 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: 1.7→60.5 Å / Num. obs: 72568 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 22.93 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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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: 1.7→35.509 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 3652 5 %
Rwork0.1695 --
obs0.1706 72462 99.25 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.304 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 32.05 Å2
Baniso -1Baniso -2Baniso -3
1-5.0809 Å20 Å29.7139 Å2
2--0.3579 Å20 Å2
3----5.4388 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 0 444 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014322
X-RAY DIFFRACTIONf_angle_d1.115863
X-RAY DIFFRACTIONf_dihedral_angle_d11.7881663
X-RAY DIFFRACTIONf_chiral_restr0.07668
X-RAY DIFFRACTIONf_plane_restr0.005749
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1851X-RAY DIFFRACTIONPOSITIONAL
12B1851X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72240.29671380.28812670X-RAY DIFFRACTION100
1.7224-1.7460.33541270.28232638X-RAY DIFFRACTION100
1.746-1.77090.26781400.25992667X-RAY DIFFRACTION99
1.7709-1.79730.28151380.24672648X-RAY DIFFRACTION100
1.7973-1.82540.28571320.22862668X-RAY DIFFRACTION100
1.8254-1.85530.25691300.2072625X-RAY DIFFRACTION100
1.8553-1.88730.22071240.1932695X-RAY DIFFRACTION100
1.8873-1.92170.22791420.17592644X-RAY DIFFRACTION100
1.9217-1.95860.19771340.17062658X-RAY DIFFRACTION100
1.9586-1.99860.2131380.17012678X-RAY DIFFRACTION100
1.9986-2.0420.21781500.17082616X-RAY DIFFRACTION100
2.042-2.08950.22011410.17612697X-RAY DIFFRACTION100
2.0895-2.14180.19671440.16452622X-RAY DIFFRACTION100
2.1418-2.19970.1951490.16712653X-RAY DIFFRACTION100
2.1997-2.26440.20751600.15622619X-RAY DIFFRACTION100
2.2644-2.33750.16371380.1572644X-RAY DIFFRACTION99
2.3375-2.4210.21831460.15432641X-RAY DIFFRACTION100
2.421-2.51790.20351360.16412668X-RAY DIFFRACTION99
2.5179-2.63250.19051640.16832604X-RAY DIFFRACTION99
2.6325-2.77120.19251290.15932643X-RAY DIFFRACTION99
2.7712-2.94480.15481470.1582658X-RAY DIFFRACTION99
2.9448-3.1720.16911340.16442617X-RAY DIFFRACTION99
3.172-3.4910.17711400.16812654X-RAY DIFFRACTION99
3.491-3.99550.17061540.1572612X-RAY DIFFRACTION98
3.9955-5.03170.15021340.14462644X-RAY DIFFRACTION99
5.0317-35.51680.2061430.18512627X-RAY DIFFRACTION96
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)
10.5208-0.3399-0.3480.3522-0.03210.75720.01750.0255-0.04720.0254-0.00820.0556-0.04230.00490.01230.058-0.0159-0.01190.0596-0.00510.06965.4482-9.004666.5129
20.29960.1691-0.27970.80440.42650.7385-0.0198-0.02050.0736-0.0430.03250.08580.0510.0102-0.00240.08880.0546-0.00730.11740.03440.124816.739216.293225.7137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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