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- PDB-7jxv: ANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia ... -

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Basic information

Entry
Database: PDB / ID: 7jxv
TitleANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia protein) bound to ubiquitin
Components
  • Phosphatidylinositol-binding clathrin assembly protein
  • Ubiquitin
KeywordsENDOCYTOSIS / Complex
Function / homology
Function and homology information


RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / 1-phosphatidylinositol binding / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / amyloid-beta clearance by transcytosis / extrinsic component of presynaptic endocytic zone membrane / regulation of protein transport ...RND3 GTPase cycle / membrane bending / vesicle cargo loading / endosome to plasma membrane transport vesicle / 1-phosphatidylinositol binding / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / amyloid-beta clearance by transcytosis / extrinsic component of presynaptic endocytic zone membrane / regulation of protein transport / positive regulation of amyloid precursor protein catabolic process / clathrin coat of coated pit / clathrin heavy chain binding / regulation of synaptic vesicle transport / synaptic vesicle maturation / regulation of vesicle size / postsynaptic endocytic zone / Golgi Associated Vesicle Biogenesis / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / positive regulation of dendrite extension / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / Clathrin-mediated endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / positive regulation of axonogenesis / positive regulation of Ras protein signal transduction / regulation of amyloid precursor protein catabolic process / clathrin-coated vesicle / endosomal transport / low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta formation / neurofibrillary tangle / clathrin binding / dendrite morphogenesis / parallel fiber to Purkinje cell synapse / regulation of endocytosis / hemopoiesis / synaptic vesicle endocytosis / regulation of synaptic vesicle endocytosis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / negative regulation of protein localization to plasma membrane / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / vesicle-mediated transport / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / clathrin-coated pit / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / phosphatidylinositol-4,5-bisphosphate binding / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation
Similarity search - Function
ANTH domain superfamily / Clathrin coat assembly protein AP180-like / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / ENTH/VHS / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : ...ANTH domain superfamily / Clathrin coat assembly protein AP180-like / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / ENTH/VHS / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol-binding clathrin assembly protein / Polyubiquitin-C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsPashkova, N. / Gakhar, L. / Schnicker, N.J. / Piper, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM058202 United States
CitationJournal: Elife / Year: 2021
Title: ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals.
Authors: Pashkova, N. / Gakhar, L. / Yu, L. / Schnicker, N.J. / Minard, A.Y. / Winistorfer, S. / Johnson, I.E. / Piper, R.C.
History
DepositionAug 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)41,8982
Polymers41,8982
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, NMR titration confirmed 1:1 ratio
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.068, 94.068, 91.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

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Components

#1: Protein Phosphatidylinositol-binding clathrin assembly protein / Clathrin assembly lymphoid myeloid leukemia protein / rCALM


Mass: 33321.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Picalm, Calm / Production host: Escherichia coli (E. coli) / References: UniProt: O55012
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6, 0.2 M NaCl, 20% w/v MPEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→18.83 Å / Num. obs: 17581 / % possible obs: 99.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 40.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.027 / Rrim(I) all: 0.1 / Net I/σ(I): 22.1 / Num. measured all: 238917 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.4413.90.942433317490.9180.260.9753.296.5
8.79-18.838.50.03930493600.9990.0130.04250.290

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.15data scaling
PHASERphasing
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 3ZYK

1ubq

3zyk


Resolution: 2.35→18.83 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 870 4.99 %
Rwork0.2062 16562 -
obs0.2093 17432 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.93 Å2
Refinement stepCycle: LAST / Resolution: 2.35→18.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 0 97 2836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01372791
X-RAY DIFFRACTIONf_angle_d1.6333761
X-RAY DIFFRACTIONf_chiral_restr0.0708433
X-RAY DIFFRACTIONf_plane_restr0.0089481
X-RAY DIFFRACTIONf_dihedral_angle_d19.15131060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.50.36851180.25072677X-RAY DIFFRACTION97.83
2.5-2.690.33431100.26582782X-RAY DIFFRACTION100
2.69-2.960.34821790.25522703X-RAY DIFFRACTION99.97
2.96-3.390.33241400.24922771X-RAY DIFFRACTION99.9
3.39-4.260.26071610.1912734X-RAY DIFFRACTION98.07
4.26-18.830.18531620.15942895X-RAY DIFFRACTION98.68

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