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- PDB-4xol: Observing the overall rocking motion of a protein in a crystal - ... -

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Basic information

Entry
Database: PDB / ID: 4xol
TitleObserving the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals.
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


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 ...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 / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Vif-mediated degradation of APOBEC3G
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsCoquelle, N. / Peixiang, M. / Schanda, P. / Colletier, J.P.
CitationJournal: Nat Commun / Year: 2015
Title: Observing the overall rocking motion of a protein in a crystal.
Authors: Ma, P. / Xue, Y. / Coquelle, N. / Haller, J.D. / Yuwen, T. / Ayala, I. / Mikhailovskii, O. / Willbold, D. / Colletier, J.P. / Skrynnikov, N.R. / Schanda, P.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4817
Polymers17,1542
Non-polymers3275
Water18010
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7734
Polymers8,5771
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7083
Polymers8,5771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.946, 104.946, 104.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11B-206-

HOH

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Components

#1: Protein Ubiquitin / Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.33 / Details: 100mM MES pH 6.33, 20% PEG 3350, 100mM Zn Acetate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.91→34.98 Å / Num. obs: 4656 / % possible obs: 98.83 % / Redundancy: 5.1 % / Rsym value: 0.06642 / Net I/σ(I): 16.46
Reflection shellResolution: 2.91→3.013 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.7768 / Mean I/σ(I) obs: 2.11 / % possible all: 99.34

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N30

3n30


Resolution: 2.91→34.98 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 466 10.01 %
Rwork0.2367 --
obs0.2399 4656 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 5 10 1191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051188
X-RAY DIFFRACTIONf_angle_d0.9331601
X-RAY DIFFRACTIONf_dihedral_angle_d15.436467
X-RAY DIFFRACTIONf_chiral_restr0.036194
X-RAY DIFFRACTIONf_plane_restr0.005205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9096-3.33030.34491500.35691346X-RAY DIFFRACTION99
3.3303-4.19470.30251550.26621385X-RAY DIFFRACTION99
4.1947-34.98450.23371610.19671459X-RAY DIFFRACTION98
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)
14.89290.427-5.02472.03422.38447.4001-1.70450.0184-0.18720.18111.57844.1002-0.3192-1.5173-0.08430.5576-0.04690.17261.29420.26780.8056-13.7484-8.53458.3001
20.1342-0.61290.39375.8874-1.16880.7130.07040.88230.235-1.2620.25051.8112-0.0161-1.68692.06940.6055-0.3517-0.05431.3731-0.16621.019-18.8777-7.03146.8722
36.31192.13282.94362.01450.93961.6539-0.676-0.43380.8757-1.18490.93990.8754-1.39452.0825-0.47750.4111-0.19880.12610.48-0.22450.5188-2.8473-3.22114.2094
47.7616-0.75161.0276.0113-2.00978.9748-0.19150.59250.893-0.10111.02510.5471-1.3387-0.3871-0.77470.53260.0225-0.03270.61560.09750.6052-14.8013.47564.5038
51.27960.9808-2.46462.2098-2.42494.8843-0.084-2.28711.58374.3664-0.5701-0.7091-2.78310.535-1.38291.15860.3638-0.09240.7776-0.22740.8368-6.94652.105114.1772
64.41337.48150.5382.00570.8025.08710.22-3.937-2.35672.85421.3916-0.18140.0846-1.5110.65770.7004-0.1627-0.18210.94810.66951.1403-3.9665-6.824212.6585
78.2679-6.40470.76674.9287-0.6105-0.0444-1.14820.2261.76090.60191.4123-0.91880.353-2.9525-0.13481.03370.38250.0441.16860.3220.6847-16.7905-1.15412.535
84.67330.1792-0.01164.60460.1824.35620.71740.90250.16680.46310.0091-1.7326-0.19690.5198-0.10830.9105-0.0103-0.15970.76210.00910.7475-28.920935.580936.5017
95.1843-0.80651.26914.27810.84655.29450.27710.1355-0.12430.0986-0.4425-0.47360.03070.1368-0.03420.73460.1862-0.06490.8582-0.05650.722-26.00330.106543.5139
107.7391-0.09552.0842.27741.00774.84140.6072-0.4401-0.35150.5031-0.19020.04970.33110.1672-0.51460.67970.1058-0.1530.846-0.15830.5986-34.368131.062842.1765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 17 through 22 )
4X-RAY DIFFRACTION4chain 'A' and (resid 23 through 44 )
5X-RAY DIFFRACTION5chain 'A' and (resid 45 through 56 )
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 64 )
7X-RAY DIFFRACTION7chain 'A' and (resid 65 through 72 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 49 )
10X-RAY DIFFRACTION10chain 'B' and (resid 50 through 72 )

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