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- PDB-2y5b: Structure of USP21 in complex with linear diubiquitin-aldehyde -

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Basic information

Entry
Database: PDB / ID: 2y5b
TitleStructure of USP21 in complex with linear diubiquitin-aldehyde
Components
  • UBIQUITIN
  • UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21
KeywordsPROTEIN BINDING/HYDROLASE / PROTEIN BINDING-HYDROLASE COMPLEX / UBIQUITIN / UBIQUITIN SPECIFIC PROTEASE / USP / NEDD8 / ISG15 / CELL SIGNALING
Function / homology
Function and homology information


deNEDDylase activity / symbiont entry into host cell via disruption of host cell glycocalyx / TNFR1-induced proapoptotic signaling / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / TNFR1-induced NF-kappa-B signaling pathway / cysteine-type peptidase activity / transcription initiation-coupled chromatin remodeling / Regulation of TNFR1 signaling ...deNEDDylase activity / symbiont entry into host cell via disruption of host cell glycocalyx / TNFR1-induced proapoptotic signaling / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / TNFR1-induced NF-kappa-B signaling pathway / cysteine-type peptidase activity / transcription initiation-coupled chromatin remodeling / Regulation of TNFR1 signaling / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transcription coactivator activity / Ub-specific processing proteases / proteolysis / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like ...: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Cysteine proteinases / Cathepsin B; Chain A / Pectin lyase fold / Pectin lyase fold/virulence factor / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Ubiquitin carboxyl-terminal hydrolase 21
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYe, Y. / Akutsu, M. / Reyes-Turcu, F. / Enchev, R.I. / Wilkinson, K.D. / Komander, D.
CitationJournal: Embo Rep. / Year: 2011
Title: Polyubiquitin Binding and Cross-Reactivity in the Usp Domain Deubiquitinase Usp21.
Authors: Ye, Y. / Akutsu, M. / Reyes-Turcu, F. / Enchev, R.I. / Wilkinson, K.D. / Komander, D.
History
DepositionJan 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21
B: UBIQUITIN
E: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21
F: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,17418
Polymers117,8914
Non-polymers1,28414
Water46826
1
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21
B: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,77911
Polymers58,9452
Non-polymers8349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-92 kcal/mol
Surface area21390 Å2
MethodPISA
2
E: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21
F: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3957
Polymers58,9452
Non-polymers4505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-77.1 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.870, 102.200, 86.800
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21 / USP21 / DEUBIQUITINATING ENZYME 21 / UBIQUITIN THIOLESTERASE 21 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 21


Mass: 41744.570 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 196-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 PLYSS
References: UniProt: Q9UK80, EC: 3.1.2.15, ubiquitinyl hydrolase 1
#2: Protein UBIQUITIN / DIUBIQUITIN


Mass: 17200.750 Da / Num. of mol.: 2 / Fragment: LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: NON-CLEAVABLE LINEAR DIUBIQUITIN ALDEHYDE WITH G76H MUTATION
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTYB2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 PLYSS / References: UniProt: P0CG47
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, GLY 76 TO HIS ENGINEERED RESIDUE IN CHAIN F, GLY 76 TO HIS
Nonpolymer detailsAMINO-ACETALDEHYDE (GLZ): COVALENTLY LINKED TO CYS221 IN CHAIN A, E

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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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7.4 / Details: 15% PEG8000, 0.2 M NH4SO4, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→49.8 Å / Num. obs: 24840 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0098refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HD5 AND 1UBQ

2hd5

1ubq


Resolution: 2.7→45 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.829 / SU B: 14.82 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. COVALENT LINK BETWEEN C221 IN CHAIN A,E AND GLZ152 IN CHAIN B,F.
RfactorNum. reflection% reflectionSelection details
Rfree0.27859 1267 5.1 %RANDOM
Rwork0.2158 ---
obs0.21898 23530 90.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20.15 Å2
2--1.23 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7093 0 62 26 7181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0217274
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.9739859
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1325930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11223.742310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.497151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.891550
X-RAY DIFFRACTIONr_chiral_restr0.0630.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215456
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 75 -
Rwork0.279 1641 -
obs--84.78 %

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