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- PDB-3ldz: Crystal structure of human STAM1 VHS domain in complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 3ldz
TitleCrystal structure of human STAM1 VHS domain in complex with ubiquitin
Components
  • Signal transducing adapter molecule 1
  • Ubiquitin
KeywordsPROTEIN TRANSPORT / ubiquitin-binding / Cytoplasm / Ubl conjugation / Endosome / Membrane / SH3 domain / Transport
Function / homology
Function and homology information


ESCRT-0 complex / regulation of extracellular exosome assembly / : / : / protein modification process => GO:0036211 / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / positive regulation of exosomal secretion / membrane fission / multivesicular body assembly / ubiquitin-like protein ligase binding ...ESCRT-0 complex / regulation of extracellular exosome assembly / : / : / protein modification process => GO:0036211 / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / positive regulation of exosomal secretion / membrane fission / multivesicular body assembly / ubiquitin-like protein ligase binding / RHOU GTPase cycle / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / cytosolic ribosome / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / phosphatidylinositol binding / 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 / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex
Similarity search - Function
STAM1, SH3 domain / : / : / : / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS ...STAM1, SH3 domain / : / : / : / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin interaction motif / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH3 domain / Src homology 3 domains / : / SH3-like domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Src homology 3 (SH3) domain profile. / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Alpha Horseshoe / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / Signal transducing adapter molecule 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsRen, X. / Hurley, J.H.
CitationJournal: Embo J. / Year: 2010
Title: VHS domains of ESCRT-0 cooperate in high-avidity binding to polyubiquitinated cargo.
Authors: Ren, X. / Hurley, J.H.
History
DepositionJan 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Ubiquitin
A: Signal transducing adapter molecule 1
D: Signal transducing adapter molecule 1
B: Signal transducing adapter molecule 1
C: Signal transducing adapter molecule 1
E: Ubiquitin
G: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)87,5457
Polymers87,5457
Non-polymers00
Water00
1
A: Signal transducing adapter molecule 1


Theoretical massNumber of molelcules
Total (without water)15,6571
Polymers15,6571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal transducing adapter molecule 1
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)23,9632
Polymers23,9632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Ubiquitin
C: Signal transducing adapter molecule 1


Theoretical massNumber of molelcules
Total (without water)23,9632
Polymers23,9632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Signal transducing adapter molecule 1
G: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)23,9632
Polymers23,9632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.610, 112.130, 68.660
Angle α, β, γ (deg.)90.000, 99.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin


Mass: 8305.532 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#2: Protein
Signal transducing adapter molecule 1 / STAM-1


Mass: 15657.017 Da / Num. of mol.: 4 / Fragment: Human STAM1 VHS domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92783

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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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Na thiocyanate, 20% PEG3350, 0.1M imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2009 / Details: mirrors
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→67.732 Å / Num. all: 30668 / Num. obs: 30561 / % possible obs: 95.5 % / Redundancy: 3.6 % / Limit h max: 25 / Limit h min: -25 / Limit k max: 43 / Limit k min: 0 / Limit l max: 26 / Limit l min: 0
Reflection scaleGroup code: 1
Reflection shellResolution: 2.6→37.9 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2964 / Rsym value: 0.37 / % possible all: 93.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.04
Highest resolutionLowest resolution
Rotation2.6 Å37.96 Å
Translation2.6 Å37.96 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
TNTrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37.96 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 971 3.18 %RANDOM
Rwork0.225 ---
obs0.226 30560 --
all-30561 --
Displacement parametersBiso max: 169.54 Å2 / Biso mean: 75.099 Å2 / Biso min: 27.96 Å2
Baniso -1Baniso -2Baniso -3
1--10.168 Å20 Å2-5.235 Å2
2---14.038 Å20 Å2
3---24.206 Å2
Refine analyzeLuzzati coordinate error obs: 0.424 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 0 0 6112
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.276 85 2.87 %
Rwork0.258 2879 -
all0.259 2964 -
obs-2964 -

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