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- PDB-9ckx: Crystal structure of Dsk2 Sti1 domain bound to a transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 9ckx
TitleCrystal structure of Dsk2 Sti1 domain bound to a transmembrane domain
ComponentsUbiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2
KeywordsCHAPERONE / Membrane protein Chaperone Sti1 Ubiquilin
Function / homology
Function and homology information


spindle pole body duplication / Toxicity of tetanus toxin (tetX) / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / trans-Golgi Network Vesicle Budding / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex ...spindle pole body duplication / Toxicity of tetanus toxin (tetX) / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / trans-Golgi Network Vesicle Budding / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / protein localization to vacuole / zymogen granule membrane / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / eosinophil degranulation / regulation of exocytosis / SNAP receptor activity / SNARE complex / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle fusion / regulation of vesicle-mediated transport / calcium-ion regulated exocytosis / Glutamate Neurotransmitter Release Cycle / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / neuron projection terminus / syntaxin binding / syntaxin-1 binding / clathrin-coated vesicle / Other interleukin signaling / Sensory processing of sound by inner hair cells of the cochlea / SNARE complex assembly / K48-linked polyubiquitin modification-dependent protein binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Golgi Associated Vesicle Biogenesis / Insulin processing / exocytosis / phosphorelay signal transduction system / synaptic vesicle exocytosis / synaptic vesicle endocytosis / response to glucose / vesicle-mediated transport / ERAD pathway / SNARE binding / secretory granule membrane / secretory granule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of insulin secretion / trans-Golgi network / clathrin-coated endocytic vesicle membrane / phospholipid binding / long-term synaptic potentiation / cellular response to insulin stimulus / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / protein-macromolecule adaptor activity / vesicle / membrane fusion / calmodulin binding / neuron projection / intracellular membrane-bounded organelle / synapse / perinuclear region of cytoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / : / : / UBA/TS-N domain / Ubiquitin associated domain ...Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / : / : / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-domain-containing protein / Response regulator / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesMetschnikowia bicuspidata (fungus)
Myxococcus xanthus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsWohlever, M.L. / Binsabaan, S. / Sankaran, B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CAREER 2343131 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM137904 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169-01 United States
CitationJournal: Biorxiv / Year: 2024
Title: The structural and biophysical basis of substrate binding to the hydrophobic groove in Ubiquilin Sti1 domains.
Authors: Onwunma, J. / Binsabaan, S. / Allen, S.P. / Sankaran, B. / Wohlever, M.L.
History
DepositionJul 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2
B: Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2


Theoretical massNumber of molelcules
Total (without water)48,8392
Polymers48,8392
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-75 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.410, 63.920, 67.430
Angle α, β, γ (deg.)90.000, 98.830, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2


Mass: 24419.381 Da / Num. of mol.: 2
Mutation: I98A,I102A,I106A,I108A,I110A,I111A (Uniprot Vamp2 numbering) in the Vamp2 segment
Source method: isolated from a genetically manipulated source
Details: The fusion construct consisted of the Sti1 domain of M. bicupsidata Dsk2 (residues 165-234) followed by the receiver domain of M. xanthus FrzS (residues 3-124) and a variant of the Vamp2 ...Details: The fusion construct consisted of the Sti1 domain of M. bicupsidata Dsk2 (residues 165-234) followed by the receiver domain of M. xanthus FrzS (residues 3-124) and a variant of the Vamp2 transmembrane domain (MMIALGVACAIALAIAAVYF). The linker between the Sti1 and FrzS domain is WGS and the linker between the FrzS domain and transmembrane domain is GNS.
Source: (gene. exp.) Metschnikowia bicuspidata (fungus), (gene. exp.) Myxococcus xanthus (bacteria), (gene. exp.) Homo sapiens (human)
Gene: METBIDRAFT_39938, N3T43_21095, VAMP2, SYB2 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1A0HF11, UniProt: A0AA46P9Z6, UniProt: P63027
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.5% MPD, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→46.13 Å / Num. obs: 36912 / % possible obs: 93.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 37.53 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Net I/σ(I): 17.7
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 6 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4887 / Rpim(I) all: 0.367 / % possible all: 85.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIX1.14_3260refinement
PHENIXphasing
Cootmodel building
MolProbitymodel building
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→46.13 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3675 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 1854 5.03 %
Rwork0.22 35021 -
obs0.2207 36875 93.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.45 Å2
Refinement stepCycle: LAST / Resolution: 1.98→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 0 124 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493442
X-RAY DIFFRACTIONf_angle_d0.80024632
X-RAY DIFFRACTIONf_chiral_restr0.0469514
X-RAY DIFFRACTIONf_plane_restr0.0051616
X-RAY DIFFRACTIONf_dihedral_angle_d3.00412156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.3641470.32382796X-RAY DIFFRACTION99.29
2.03-2.090.28511210.30712150X-RAY DIFFRACTION74.19
2.09-2.160.34781480.28762857X-RAY DIFFRACTION99.24
2.16-2.240.32661460.28652855X-RAY DIFFRACTION99.5
2.24-2.330.27171290.2772120X-RAY DIFFRACTION73.79
2.33-2.430.29861480.25142848X-RAY DIFFRACTION99.57
2.43-2.560.30991500.24622886X-RAY DIFFRACTION99.61
2.56-2.720.26661150.25192573X-RAY DIFFRACTION87.96
2.72-2.930.26741620.24972859X-RAY DIFFRACTION99.11
2.93-3.230.24321640.23832843X-RAY DIFFRACTION98.85
3.23-3.690.24521300.21652524X-RAY DIFFRACTION92.64
3.69-4.650.19391240.17442790X-RAY DIFFRACTION94.7
4.65-46.130.16551700.18372920X-RAY DIFFRACTION98.66
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)
13.987167107060.0661228252240.3076506243714.25010524315-2.619830485413.090959568590.0396032126683-0.273382933821-0.6368923529340.110762546992-0.3819677794390.378966852523-0.293261984506-0.3297271085430.3105250176740.566265874155-0.03091871821-0.1191383684290.418446423522-0.01696452581590.55266944349121.424948763843.0245368193-2.86832187202
21.980980742871.38129091376-0.5888907432972.64308338799-0.3690784299617.106549771390.213970597648-0.3119822937890.684924315269-0.0777025364365-0.1495009755870.129750866744-0.3246788453-0.2224433865860.02211834504940.369620329158-0.00206886195023-0.04759844958460.305964745892-0.01372502498980.38085594583337.303224400557.5809344872-7.97042108004
32.773277759372.27515817064-2.794621946923.72230969559-3.92657207144.442127461520.198083926560.96183499911-0.338896728063-0.684716914338-0.05075030127330.437998242636-0.25519759534-0.803573046405-0.2067552735440.7442322371860.100673392835-0.1159842517360.468340091332-0.06418951462960.39367798955732.841815200245.9593881489-14.9095311637
46.708512920550.3810050791253.46666596266.40738404755-3.12133617873.528931313040.5668098767830.598255496241-0.247072293885-0.4748280473320.09748061772220.5951772345051.11698382299-0.0152146860218-0.1615694366580.4680395260720.0088141844363-0.09837185564510.305986832495-0.01458271142160.33956921672831.570069605735.89478437341.52560968271
53.073933262010.738467052816-0.6178970795255.399913172040.3166478995739.545772984950.0615962114531-0.0144847064843-0.002268212301750.677170997176-0.02381620780320.01441018567490.6541958129250.0444609719095-0.04160419322440.7506909046440.0227863703970.113894609780.3315998880510.004272778288550.24761771540927.482325468740.441106671533.7534863661
61.781449991020.30096195106-2.036155471262.25076476565-1.884067115246.316466429960.1443448778310.228815015568-0.2137137323760.448916706402-0.00334356891284-0.0552386936233-0.254410531319-0.538232228559-0.1625153514890.267791349486-0.0350157379063-0.0364893331830.239245989207-0.03943971243640.20229354053132.046093727544.85428115699.14205142233
73.58735629857-3.76025220104-0.6647810056614.800378458290.4588778950993.822415787460.239529885947-0.1527224844030.1063815861140.284784272684-0.2051614471820.0115051194238-0.674538752483-0.275017628019-0.05154771840640.4925268433380.0299900121251-0.0848358164070.424727070725-0.03753218250120.51200466892534.71891583548.046313447412.5194727621
87.035976573292.45541666273-2.39633368875.44723271341-4.949591990695.020007543940.0699147007341-0.0591688204573-0.3458087768580.115983757107-0.244575654534-0.2459103127850.841675401947-0.1327130821070.3574072113340.3528283297830.00455481339858-0.04894359885520.289792566139-0.01356335645090.34790983845242.139809631933.3992506878-2.35866755877
93.91208825331-3.83231551456-0.1327459860527.293529185720.821426474492-0.0108028525286-0.149146538102-0.5152750428020.2289595754960.4910838785470.151528759714-0.702490519776-0.09082484186120.09953690504120.09585071876430.406639573261-0.0483901208914-0.1109117925620.3994467104350.03610654307830.43020767326240.542900393449.83391654992.6018569584
102.56970384445-0.7918788590711.255773617266.12011325803-0.01991170618684.70457832924-0.281926620303-0.009872918802311.442757663390.06644871121620.05774673465110.200450667862-0.2123582288340.09626116052530.1248702938140.283999922178-0.0190057121040.02800330150220.382129218521-0.05231485223510.989148197214.4677779251757.47760243344.52397262778
118.928232936490.1370926765740.3848489076644.951090261680.0005090513081654.41760820303-0.05553126815710.5883037983730.476296516189-0.3016290495090.03807629699410.8512396782970.0611208093192-0.1496557152140.1188885416570.24900882206-0.00962163128031-0.05207446124710.3687261845090.02354469027730.754355163478-3.0529446003948.4348100278-2.37429363553
124.84893175369-1.07779456657-0.4248066481051.4726292597-0.09961114452860.465038389816-0.155530362199-0.44342616113-0.3562968861520.07819045704170.08688680671810.575024217745-0.0482527014569-0.03975411184040.08547501023660.257615812247-0.01639307849520.00558193612420.283259564021-0.0201004280540.41791936844916.282063619145.06701957321.77812789642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 75 )
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 183 )
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 222 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 44 )
9X-RAY DIFFRACTION9chain 'B' and (resid 45 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 112 )
11X-RAY DIFFRACTION11chain 'B' and (resid 113 through 168 )
12X-RAY DIFFRACTION12chain 'B' and (resid 169 through 222 )

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