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- PDB-3zym: Structure of CALM (PICALM) in complex with VAMP8 -

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Basic information

Entry
Database: PDB / ID: 3zym
TitleStructure of CALM (PICALM) in complex with VAMP8
ComponentsPHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8
KeywordsENDOCYTOSIS / SYNAPTOBREVIN / VAMP2 / VAMP3 / AP180 / PLASMA MEMBRANE / ADAPTOR PROTEIN
Function / homology
Function and homology information


zymogen granule exocytosis / positive regulation of pancreatic amylase secretion / mucin granule / trans-Golgi Network Vesicle Budding / RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / zymogen granule / basolateral part of cell ...zymogen granule exocytosis / positive regulation of pancreatic amylase secretion / mucin granule / trans-Golgi Network Vesicle Budding / RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / zymogen granule / basolateral part of cell / 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 / Lysosome Vesicle Biogenesis / extrinsic component of presynaptic endocytic zone membrane / zymogen granule membrane / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle transport / amyloid-beta clearance by transcytosis / clathrin heavy chain binding / clathrin coat of coated pit / mucus secretion / regulation of vesicle size / synaptic vesicle maturation / vesicle fusion / negative regulation of protein localization to cell surface / Golgi Associated Vesicle Biogenesis / negative regulation of receptor-mediated endocytosis / SNARE complex / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / SNAP receptor activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / basal part of cell / 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 / syntaxin binding / ER-Phagosome pathway / parallel fiber to Purkinje cell synapse / clathrin-coated vesicle / dendrite morphogenesis / regulation of synaptic vesicle endocytosis / SNARE complex assembly / endosomal transport / neurofibrillary tangle / positive regulation of axonogenesis / positive regulation of amyloid-beta formation / low-density lipoprotein particle receptor binding / clathrin binding / regulation of endocytosis / hemopoiesis / synaptic vesicle endocytosis / autophagosome maturation / negative regulation of protein localization to plasma membrane / phagocytic vesicle / clathrin-coated pit / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / receptor-mediated endocytosis / axonogenesis / SNARE binding / secretory granule / establishment of localization in cell / tau protein binding / Schaffer collateral - CA1 synapse / receptor internalization / recycling endosome / cellular response to type II interferon / small GTPase binding / multicellular organismal-level iron ion homeostasis / SH3 domain binding / endocytosis / protein transport / synaptic vesicle / late endosome membrane / regulation of protein localization / presynaptic membrane / early endosome membrane / midbody / protein-containing complex assembly / basolateral plasma membrane / defense response to virus / postsynaptic membrane / intracellular iron ion homeostasis / vesicle / postsynapse / membrane fusion / postsynaptic density / early endosome
Similarity search - Function
ANTH domain / ANTH domain superfamily / Clathrin coat assembly protein AP180-like / AP180 N-terminal homology (ANTH) domain / ANTH domain / Synaptobrevin/Vesicle-associated membrane protein / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Synaptobrevin-like ...ANTH domain / ANTH domain superfamily / Clathrin coat assembly protein AP180-like / AP180 N-terminal homology (ANTH) domain / ANTH domain / Synaptobrevin/Vesicle-associated membrane protein / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / 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
PHOSPHATE ION / Phosphatidylinositol-binding clathrin assembly protein / Vesicle-associated membrane protein 8
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 15, 2017Group: Source and taxonomy
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8
B: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8
C: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,59316
Polymers105,3763
Non-polymers1,21713
Water8,521473
1
A: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5946
Polymers35,1251
Non-polymers4695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4995
Polymers35,1251
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4995
Polymers35,1251
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.051, 100.260, 104.021
Angle α, β, γ (deg.)90.00, 118.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-3015-

HOH

21B-3064-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND NOT (RESSEQ 32 OR RESSEQ 65 OR...
211CHAIN B
311CHAIN C
112CHAIN B AND RESSEQ 1015:1025
212CHAIN C
113CHAIN A AND RESSEQ 1036:1038
213CHAIN B

NCS ensembles :
ID
1
2
3

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Components

#1: Protein PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN, VESICLE-ASSOCIATED MEMBRANE PROTEIN 8 / CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN / RCALM / VAMP-8 / ENDOBREVIN / EDB / CHIMERA ...CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN / RCALM / VAMP-8 / ENDOBREVIN / EDB / CHIMERA OF THE CALM ANTH DOMAIN AND THE VAMP8 SNARE DOMAIN


Mass: 35125.348 Da / Num. of mol.: 3
Fragment: PARTIAL ANTH DOMAIN OF CALM, RESIDUES 1-264, PARTIAL SNARE DOMAIN OF VAMP8, RESIDUES 11-41
Source method: isolated from a genetically manipulated source
Details: RESIDUES 11-41 OF VAMP8 ARE FUSED TO RESIDUES 1-264 OF CALM VIA A 8 RESIDUE LINKER
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat), (gene. exp.) MUS MUSCULUS (house mouse)
Plasmid: PGEX 4T2 CALMANTH(1-289) VAMP8(1- 76) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: O55012, UniProt: O70404
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GSPIGIP SEQUENCE IS RESIDUAL FROM AFFINITY TAG AND CLONING. CONTAINS A KNOWN SEQUENCE ...N-TERMINAL GSPIGIP SEQUENCE IS RESIDUAL FROM AFFINITY TAG AND CLONING. CONTAINS A KNOWN SEQUENCE VARIANT (VAMP8 S36A)

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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: 3.49 Å3/Da / Density % sol: 64.75 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
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 PHOSPHATE-CITRATE ...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 PHOSPHATE-CITRATE PH 4.2, 200 MM NACL, 50% (V/V) PEG-200) 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: 2→91.1 Å / Num. obs: 93133 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 33.81 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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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: 2.03→45.573 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 4667 5 %
Rwork0.1807 --
obs0.1815 93104 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.15 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 42.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.0877 Å20 Å22.8613 Å2
2---3.7334 Å20 Å2
3---2.6457 Å2
Refinement stepCycle: LAST / Resolution: 2.03→45.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6713 0 71 473 7257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086987
X-RAY DIFFRACTIONf_angle_d0.9139417
X-RAY DIFFRACTIONf_dihedral_angle_d12.9822655
X-RAY DIFFRACTIONf_chiral_restr0.0631076
X-RAY DIFFRACTIONf_plane_restr0.0041185
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1918X-RAY DIFFRACTIONPOSITIONAL
12B1918X-RAY DIFFRACTIONPOSITIONAL0.066
13C1916X-RAY DIFFRACTIONPOSITIONAL0.048
21B84X-RAY DIFFRACTIONPOSITIONAL
22C84X-RAY DIFFRACTIONPOSITIONAL0.02
31A20X-RAY DIFFRACTIONPOSITIONAL
32B20X-RAY DIFFRACTIONPOSITIONAL0.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.05310.34311620.28142933X-RAY DIFFRACTION100
2.0531-2.07720.30321560.27492959X-RAY DIFFRACTION100
2.0772-2.10260.2881420.25462921X-RAY DIFFRACTION100
2.1026-2.12920.2511550.24372972X-RAY DIFFRACTION100
2.1292-2.15720.27521630.23292926X-RAY DIFFRACTION100
2.1572-2.18680.2361630.22122924X-RAY DIFFRACTION100
2.1868-2.2180.22521630.20722953X-RAY DIFFRACTION100
2.218-2.25110.27311410.20242911X-RAY DIFFRACTION100
2.2511-2.28630.20351560.19032941X-RAY DIFFRACTION100
2.2863-2.32380.21631520.18072950X-RAY DIFFRACTION100
2.3238-2.36380.22021700.18492935X-RAY DIFFRACTION100
2.3638-2.40680.21611600.17782939X-RAY DIFFRACTION100
2.4068-2.45310.19041450.16982929X-RAY DIFFRACTION100
2.4531-2.50320.19271540.16492968X-RAY DIFFRACTION100
2.5032-2.55760.19411210.16362973X-RAY DIFFRACTION100
2.5576-2.61710.20071700.17492918X-RAY DIFFRACTION100
2.6171-2.68250.20781580.1722926X-RAY DIFFRACTION100
2.6825-2.7550.18931660.16752931X-RAY DIFFRACTION100
2.755-2.83610.19731610.16792954X-RAY DIFFRACTION100
2.8361-2.92760.18331650.16192938X-RAY DIFFRACTION100
2.9276-3.03220.18511540.17042929X-RAY DIFFRACTION99
3.0322-3.15360.20721690.17472961X-RAY DIFFRACTION99
3.1536-3.29710.19441430.17752956X-RAY DIFFRACTION100
3.2971-3.47090.20321420.17562963X-RAY DIFFRACTION100
3.4709-3.68830.16631470.16212960X-RAY DIFFRACTION100
3.6883-3.97290.16821450.15992995X-RAY DIFFRACTION100
3.9729-4.37240.17661600.15652959X-RAY DIFFRACTION100
4.3724-5.00440.17781720.15972939X-RAY DIFFRACTION99
5.0044-6.30240.21111490.20942963X-RAY DIFFRACTION99
6.3024-45.58420.19091630.20833011X-RAY DIFFRACTION99
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)
11.47460.1177-0.332.0338-0.78431.71130.06350.21090.01130.08950.02320.19460.0057-0.1121-0.07670.11940.0258-0.02650.17630.00390.1593-41.784813.8466-28.0772
21.7074-0.4992-0.22750.92530.15540.953-0.0160.0918-0.05990.0406-0.01840.0441-0.0132-0.2090.02920.1359-0.02320.010.1486-0.02910.1830.74326.1411-38.9783
30.6493-0.1893-0.03261.5305-0.69991.41490.08340.10490.0163-0.2687-0.0908-0.09380.01510.0494-0.00190.23430.02830.02550.1908-0.02790.171-25.060826.85777.6948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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