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- PDB-2gbk: Crystal Structure of the 9-10 MoaD Insertion Mutant of Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 2gbk
TitleCrystal Structure of the 9-10 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 / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of BACH1 activity / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Gap-filling DNA repair synthesis and ligation in GG-NER / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / cytosolic ribosome / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Degradation of DVL / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome
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 conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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: 1.99 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: Advisory / Derived calculations / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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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
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)37,4394
Polymers37,4394
Non-polymers00
Water4,576254
1
A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)9,3601
Polymers9,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)9,3601
Polymers9,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)9,3601
Polymers9,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)9,3601
Polymers9,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Ubiquitin
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)18,7192
Polymers18,7192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-18 kcal/mol
Surface area8200 Å2
MethodPISA, PQS
6
B: Ubiquitin
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)18,7192
Polymers18,7192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-18 kcal/mol
Surface area8090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)30.046, 45.895, 54.382
Angle α, β, γ (deg.)79.91, 74.99, 81.33
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 1 - 80 / Label seq-ID: 1 - 80

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe monomer is believed to be the active biological assembly.

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Components

#1: Protein
Ubiquitin /


Mass: 9359.737 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 27-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, 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 Å
DetectorDate: Jul 24, 2004
RadiationMonochromator: Cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→5.8 Å / Num. all: 18012 / Num. obs: 16333 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.73 % / Rmerge(I) obs: 0.084 / Χ2: 0.96 / Net I/σ(I): 9.6 / Scaling rejects: 338
Reflection shellResolution: 1.99→2.06 Å / % possible obs: 89.8 % / Redundancy: 2.66 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.2 / Num. measured all: 4262 / Num. unique all: 1603 / Num. unique obs: 1603 / Χ2: 0.5 / % possible all: 89.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
JDirectordata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GBJ

2gbj


Resolution: 1.99→5.8 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.853 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.428 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28668 850 5.2 %RANDOM
Rwork0.24403 ---
all0.24638 18012 --
obs0.24638 16331 90.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.166 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å21.32 Å2-1.08 Å2
2---1.48 Å20.29 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.99→5.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 0 254 2851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222621
X-RAY DIFFRACTIONr_bond_other_d0.0010.021839
X-RAY DIFFRACTIONr_angle_refined_deg0.8571.9963526
X-RAY DIFFRACTIONr_angle_other_deg0.74334536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0225323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73525.462119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47615537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8011519
X-RAY DIFFRACTIONr_chiral_restr0.050.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_nbd_refined0.1570.2494
X-RAY DIFFRACTIONr_nbd_other0.1630.22065
X-RAY DIFFRACTIONr_nbtor_refined0.1510.21251
X-RAY DIFFRACTIONr_nbtor_other0.0750.21406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0860.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.230
X-RAY DIFFRACTIONr_mcbond_it0.2331.52127
X-RAY DIFFRACTIONr_mcbond_other0.0341.5662
X-RAY DIFFRACTIONr_mcangle_it0.26322640
X-RAY DIFFRACTIONr_scbond_it0.47931097
X-RAY DIFFRACTIONr_scangle_it0.7334.5886
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A471MEDIUM POSITIONAL0.150.5
2B471MEDIUM POSITIONAL0.160.5
3C471MEDIUM POSITIONAL0.160.5
4D471MEDIUM POSITIONAL0.150.5
1A613LOOSE POSITIONAL0.885
2B613LOOSE POSITIONAL0.915
3C613LOOSE POSITIONAL0.765
4D613LOOSE POSITIONAL0.945
1A471MEDIUM THERMAL0.112
2B471MEDIUM THERMAL0.12
3C471MEDIUM THERMAL0.152
4D471MEDIUM THERMAL0.152
1A613LOOSE THERMAL0.3110
2B613LOOSE THERMAL0.310
3C613LOOSE THERMAL0.3210
4D613LOOSE THERMAL0.3110
LS refinement shellResolution: 1.993→2.039 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 57 -
Rwork0.241 1014 -
obs-1071 87.71 %
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)
11.76430.11711.10412.23660.27674.56420.0359-0.16120.02320.2283-0.0439-0.07410.0413-0.0680.008-0.0804-0.03430.04440.0128-0.0213-0.08272.482-6.289-2.359
22.49030.03791.86481.88160.73914.90730.0153-0.07790.09010.08730.0018-0.08610.1444-0.0509-0.0172-0.058-0.03820.0368-0.0014-0.0072-0.0824-15.646-27.949-1.854
33.42480.20241.76382.260.84933.4093-0.02410.2182-0.1466-0.02950.03220.05630.17410.1818-0.008-0.0794-0.03950.03570.0116-0.0136-0.0933-1.01-7.32-24.537
42.2471-0.30281.96543.08331.17446.4728-0.09460.19640.1839-0.13870-0.0396-0.2806-0.00470.0946-0.0681-0.04750.0313-0.00880.0052-0.068-17.966-30.129-24.528
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 821 - 82
22BB1 - 821 - 82
33CC1 - 831 - 83
44DD1 - 801 - 80

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