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- PDB-2gbr: Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 2gbr
TitleCrystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin
ComponentsUbiquitin
KeywordsPROTEIN BINDING / LOOP INSERTION
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / 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 ...: / : / protein modification process => GO:0036211 / 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 / 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 / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / 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
: / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFerraro, D.M. / Ferraro, D.J. / Ramaswamy, S. / Robertson, A.D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structures of Ubiquitin Insertion Mutants Support Site-specific Reflex Response to Insertions Hypothesis.
Authors: Ferraro, D.M. / Ferraro, D.J. / Ramaswamy, S. / Robertson, A.D.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ref_seq_dif.details / _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
B: Ubiquitin
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,98816
Polymers27,5273
Non-polymers1,46113
Water3,405189
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5134
Polymers9,1761
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9628
Polymers9,1761
Non-polymers7877
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5134
Polymers9,1761
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Ubiquitin
hetero molecules

B: Ubiquitin
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,98816
Polymers27,5273
Non-polymers1,46113
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_575-x+1/2,-y+2,z+1/21
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-85 kcal/mol
Surface area13190 Å2
MethodPISA
5
A: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,47512
Polymers18,3512
Non-polymers1,12410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-60 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.465, 54.807, 92.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe monomer is believed to be the active biological assembly.

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Components

#1: Protein Ubiquitin


Mass: 9175.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: 24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00808 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2005
RadiationMonochromator: Cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00808 Å / Relative weight: 1
ReflectionResolution: 2→5 Å / Num. all: 14781 / Num. obs: 14696 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.86 % / Rmerge(I) obs: 0.135 / Χ2: 0.97 / Net I/σ(I): 5.9 / Scaling rejects: 429
Reflection shellResolution: 2→2.07 Å / % possible obs: 100 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.5 / Num. measured all: 5645 / Num. unique all: 1447 / Num. unique obs: 1447 / Χ2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREK9.5LDzdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
JDirectordata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GBM

2gbm


Resolution: 2→4.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.539 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28971 745 5.1 %RANDOM
Rwork0.21583 ---
all0.21938 14781 --
obs0.21938 14668 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→4.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 13 189 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221864
X-RAY DIFFRACTIONr_bond_other_d0.0010.021292
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9822515
X-RAY DIFFRACTIONr_angle_other_deg0.79533188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.29425.54283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57715372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3111511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_nbd_refined0.2130.2350
X-RAY DIFFRACTIONr_nbd_other0.1790.21277
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2822
X-RAY DIFFRACTIONr_nbtor_other0.0830.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.2131
X-RAY DIFFRACTIONr_metal_ion_refined0.2430.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4420.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.240
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4930.21
X-RAY DIFFRACTIONr_mcbond_it0.8381.51485
X-RAY DIFFRACTIONr_mcbond_other0.1421.5460
X-RAY DIFFRACTIONr_mcangle_it0.96521864
X-RAY DIFFRACTIONr_scbond_it1.7753809
X-RAY DIFFRACTIONr_scangle_it2.7464.5651
LS refinement shellResolution: 2→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 54 -
Rwork0.217 918 -
obs-972 99.9 %

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