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- PDB-4ae4: The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a novel... -

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Basic information

Entry
Database: PDB / ID: 4ae4
TitleThe UBAP1 subunit of ESCRT-I interacts with ubiquitin via a novel SOUBA domain
Components(UBIQUITIN-ASSOCIATED PROTEIN ...) x 2
KeywordsPROTEIN TRANSPORT / ENDOSOMAL SORTING / TETHERIN / VPU / HIV-1 / MONOUBIQUITIN
Function / homology
Function and homology information


ESCRT I complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / HCMV Late Events / ubiquitin binding / Late endosomal microautophagy ...ESCRT I complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / HCMV Late Events / ubiquitin binding / Late endosomal microautophagy / Budding and maturation of HIV virion / endosome membrane / intracellular membrane-bounded organelle / plasma membrane / cytoplasm / cytosol
Similarity search - Function
UBAP1 SOUBA domain / Ubiquitin-associated protein 1 / Ubiquitin-associated protein 1, C-terminal / : / Ubiquitin-associated protein 1, UBA2 domain / UMA domain / UMA domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily ...UBAP1 SOUBA domain / Ubiquitin-associated protein 1 / Ubiquitin-associated protein 1, C-terminal / : / Ubiquitin-associated protein 1, UBA2 domain / UMA domain / UMA domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ubiquitin-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsAgromayor, M. / Soler, N. / Caballe, A. / Kueck, T. / Freund, S.M. / Allen, M.D. / Bycroft, M. / Perisic, O. / Ye, Y. / McDonald, B. ...Agromayor, M. / Soler, N. / Caballe, A. / Kueck, T. / Freund, S.M. / Allen, M.D. / Bycroft, M. / Perisic, O. / Ye, Y. / McDonald, B. / Scheel, H. / Hofmann, K. / Neil, S.J.D. / Martin-Serrano, J. / Williams, R.L.
CitationJournal: Structure / Year: 2012
Title: The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain.
Authors: Agromayor, M. / Soler, N. / Caballe, A. / Kueck, T. / Freund, S.M. / Allen, M.D. / Bycroft, M. / Perisic, O. / Ye, Y. / McDonald, B. / Scheel, H. / Hofmann, K. / Neil, S.J. / Martin-Serrano, J. / Williams, R.L.
History
DepositionJan 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-ASSOCIATED PROTEIN 1
B: UBIQUITIN-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31910
Polymers27,6332
Non-polymers6868
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-21.6 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.404, 43.480, 59.413
Angle α, β, γ (deg.)102.58, 96.47, 113.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9999, -0.0035, 0.0102), (-0.0035, -1, 0.0003), (0.0102, -0.0003, -0.9999)
Vector: -0.4867, -36.2915, 82.1913)

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Components

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UBIQUITIN-ASSOCIATED PROTEIN ... , 2 types, 2 molecules AB

#1: Protein UBIQUITIN-ASSOCIATED PROTEIN 1 / UBAP-1 / UBAP1 / NASOPHARYNGEAL CARCINOMA-ASSOCIATED GENE 20 PROTEIN


Mass: 13800.384 Da / Num. of mol.: 1 / Fragment: SOUBA DOMAIN, RESIDUES 389-502 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 RIPL / References: UniProt: Q9NZ09
#2: Protein UBIQUITIN-ASSOCIATED PROTEIN 1 / UBAP-1 / UBAP1 / NASOPHARYNGEAL CARCINOMA-ASSOCIATED GENE 20 PROTEIN


Mass: 13832.384 Da / Num. of mol.: 1 / Fragment: SOUBA DOMAIN, RESIDUES 389-502 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 2 OXIDIZED SELENOMETHIONINES, B 402 AND B 449 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 RIPL / References: UniProt: Q9NZ09

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Non-polymers , 5 types, 250 molecules

#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 415 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 416 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 415 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 416 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 418 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 415 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 416 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 418 TO ALA
Sequence detailsPROTEIN IS ISOFORM 1. RESIDUES 389-502 ARE THE SOUBA DOMAIN AS DEFINED IN OUR PAPER)

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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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: NONE
Crystal growpH: 9.5
Details: 645 MM NA/K TARTRATE, 271 MM LISO4, 100 MM CHES PH 9.5, 2 MM TCEP, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980024
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980024 Å / Relative weight: 1
ReflectionResolution: 1.65→38.3 Å / Num. obs: 36253 / % possible obs: 95.9 % / Observed criterion σ(I): 1.9 / Redundancy: 3.9 % / Biso Wilson estimate: 24.61 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SOLVEviaphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.65→28.274 Å / SU ML: 0.47 / σ(F): 1.96 / Phase error: 19.9 / Stereochemistry target values: ML
Details: THE FOLLOWING TABLE REFERS TO UNMERGED ANOMALOUS DATA: FIT TO DATA USED IN REFINEMENT
RfactorNum. reflection% reflection
Rfree0.1907 1481 5 %
Rwork0.1494 --
obs0.1516 36253 95.07 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.983 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 0.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.3538 Å2-1.4206 Å2-2.059 Å2
2---0.2862 Å2-0.6781 Å2
3----1.0676 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 37 242 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161880
X-RAY DIFFRACTIONf_angle_d1.5362514
X-RAY DIFFRACTIONf_dihedral_angle_d15.768733
X-RAY DIFFRACTIONf_chiral_restr0.096272
X-RAY DIFFRACTIONf_plane_restr0.006325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67260.48491380.38332611X-RAY DIFFRACTION92
1.6726-1.69650.38061040.33162535X-RAY DIFFRACTION94
1.6965-1.72180.38561510.32432596X-RAY DIFFRACTION93
1.7218-1.74870.37851160.3032624X-RAY DIFFRACTION95
1.7487-1.77740.29841540.2362543X-RAY DIFFRACTION94
1.7774-1.8080.25471270.20812732X-RAY DIFFRACTION94
1.808-1.84090.2491090.18622516X-RAY DIFFRACTION95
1.8409-1.87630.24621230.1772669X-RAY DIFFRACTION95
1.8763-1.91460.22541220.16162648X-RAY DIFFRACTION94
1.9146-1.95620.24241480.13852555X-RAY DIFFRACTION96
1.9562-2.00170.18311600.13022588X-RAY DIFFRACTION95
2.0017-2.05180.1618990.14012729X-RAY DIFFRACTION95
2.0518-2.10720.20261340.13442607X-RAY DIFFRACTION95
2.1072-2.16920.20631430.11982684X-RAY DIFFRACTION96
2.1692-2.23920.14531280.11722572X-RAY DIFFRACTION96
2.2392-2.31920.15241500.10882628X-RAY DIFFRACTION95
2.3192-2.4120.16221490.10512681X-RAY DIFFRACTION96
2.412-2.52170.14441230.11052629X-RAY DIFFRACTION97
2.5217-2.65460.18121620.11672638X-RAY DIFFRACTION97
2.6546-2.82070.16881440.14112667X-RAY DIFFRACTION97
2.8207-3.03830.19291670.14832584X-RAY DIFFRACTION97
3.0383-3.34360.18891500.15252699X-RAY DIFFRACTION97
3.3436-3.82640.16131540.13272656X-RAY DIFFRACTION96
3.8264-4.8170.14611590.11942604X-RAY DIFFRACTION96
4.817-28.27770.2591180.21172490X-RAY DIFFRACTION90

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