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

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Basic information

Entry
Database: PDB / ID: 4xok
TitleObserving the overall rocking motion of a protein in a crystal.
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / ubiquitin / Zinc
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 / 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 PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / 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 / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Stabilization of p53 / EGFR downregulation / Negative regulation of FGFR1 signaling / Negative regulation of NOTCH4 signaling / Iron uptake and transport / G2/M Checkpoints / Translesion Synthesis by POLH / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Similarity search - Function
Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCoquelle, N. / Ma, P. / 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_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.ptnr2_symmetry / _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

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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)26,1239
Polymers25,7303
Non-polymers3926
Water1,47782
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7083
Polymers8,5771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
3
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7083
Polymers8,5771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.724, 50.364, 93.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin / / Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 3
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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20mg/ml Ubi in 20mM NH4Ac pH4.3, 50mM HEPES pH7.0, 35% PEG 1500, 25mM Zn Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→46.729 Å / Num. obs: 10207 / % possible obs: 92.96 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.08323 / Net I/σ(I): 16.04
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.1753 / % possible all: 62

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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: 3EHV

3ehv


Resolution: 2.2→9.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 32.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3236 501 5 %
Rwork0.3026 --
obs0.3037 10016 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 6 82 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071721
X-RAY DIFFRACTIONf_angle_d1.3582318
X-RAY DIFFRACTIONf_dihedral_angle_d16.114678
X-RAY DIFFRACTIONf_chiral_restr0.059279
X-RAY DIFFRACTIONf_plane_restr0.009297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.41870.37711000.33761875X-RAY DIFFRACTION75
2.4187-2.76220.36611310.33152507X-RAY DIFFRACTION99
2.7622-3.45580.33591320.30672508X-RAY DIFFRACTION98
3.4558-9.96990.27661380.27322625X-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)
10.13270.0036-0.04540.00230.00010.0223-0.12180.09550.0859-0.0753-0.10710.0602-0.1629-0.1986-0.41050.21480.3397-0.1392-0.01070.0090.2807-16.17180.8029-15.48
20.3124-0.0255-0.09950.0944-0.00270.0409-0.0071-0.23480.0644-0.16210.05310.3478-0.04240.05270.29140.40350.0475-0.14710.1254-0.03650.2307-14.41057.934-8.519
30.2871-0.16920.46280.1259-0.31870.82320.1838-0.0704-0.3535-0.0760.10710.06650.24520.01640.3840.1625-0.03760.14910.08610.3305-0.0647-14.0242-0.1498-4.7165
41.42760.36171.05580.10840.23410.89150.0705-0.2896-0.4072-0.05190.2209-0.32760.394-0.17330.3370.26150.1150.03660.4879-0.0910.3258-9.1253-6.2276-7.8211
50.0496-0.0131-0.0850.07620.10240.29840.0375-0.0364-0.02920.0906-0.005-0.07570.15310.1673-0.05770.30260.03040.01810.3959-0.04180.2173-2.50822.5162-16.8573
60.04170.0611-0.05950.25850.13040.4097-0.1361-0.0724-0.1273-0.1013-0.0859-0.15160.09580.1328-0.27750.1660.12360.06110.3429-0.11310.0863-1.3163.387-6.699
70.0035-0.0107-0.00750.02560.02880.02450.05920.04050.11540.03160.01860.09870.0268-0.04160.2286-0.4102-0.3587-0.1543-0.1175-0.24620.3228-3.45439.5842-10.0734
80.1646-0.26780.03630.4611-0.13260.22020.03450.0370.2009-0.08030.02820.1404-0.1031-0.02410.0690.32880.04280.11740.24380.07980.3838-10.795911.6719-16.6691
90.1176-0.1407-0.12320.20480.02410.4616-0.21090.09270.0509-0.1637-0.08730.1082-0.0872-0.0148-0.44790.2243-0.0517-0.03120.09910.03410.1898-10.1848-1.2506-16.3168
100.1477-0.09560.27750.3464-0.34730.58060.0029-0.21490.09370.2312-0.0945-0.2055-0.45830.3353-0.25370.25950.0173-0.04260.44460.03970.1516-6.5649-6.419-33.4495
110.18460.02170.10040.36290.17280.1802-0.1176-0.2986-0.13570.1642-0.00670.05190.10760.0758-0.64870.2541-0.00320.04250.2506-0.00840.1693-7.9794-14.8789-33.7856
120.409-0.36-0.01390.9386-0.53420.4980.08070.036-0.20530.4047-0.03290.31530.1906-0.27770.13010.2380.05340.02290.2564-0.07260.1832-12.5145-15.7427-26.9269
130.371-0.5682-0.54390.92330.9671.2689-0.160.0932-0.23290.191-0.27490.24710.3393-0.0869-0.10080.39680.0982-0.02520.3188-0.07170.2009-19.3058-7.4967-33.6983
140.3825-0.66020.30671.1745-0.4950.2925-0.06910.25820.37660.104-0.2151-0.5733-0.15980.3247-0.30370.2366-0.00760.09120.11380.0240.2407-14.2333-0.7565-37.6119
150.04670.0022-0.05530.1839-0.22450.3241-0.004-0.1645-0.06680.0791-0.03150.0850.0116-0.1927-0.09230.4276-0.124-0.03980.4160.05960.2002-13.3412-8.8688-24.188
160.69450.02110.83520.15590.01491.02360.2393-0.2813-0.0220.03750.13940.05210.0239-0.04140.45350.3760.15990.12250.40580.05910.2799-15.810228.97231.4599
170.00640.03750.01660.23170.10410.0457-0.07950.04460.0189-0.0224-0.0231-0.0476-0.08960.0678-0.2430.59720.04090.1420.16320.43790.4899-16.550736.9872-9.2452
180.2543-0.0372-0.0360.15710.07230.03550.11970.04770.0119-0.11760.00090.1793-0.3052-0.30780.49880.17640.0251-0.02530.00440.42340.0692-14.332822.54370.4503
190.0724-0.02720.03730.0927-0.00310.08880.2913-0.03940.05130.04150.0360.05150.0259-0.1608-0.08670.1983-0.01420.03420.1808-0.03510.1943-13.930422.4733-8.3554
200.34110.0501-0.30050.19280.12450.4316-0.05230.14880.0633-0.0510.0275-0.13640.2399-0.1929-0.30580.2691-0.07870.15810.45230.3440.4087-8.982127.5576-12.6201
210.1416-0.2521-0.18340.48350.33750.23490.0772-0.06220.2149-0.20950.0291-0.3543-0.20620.0924-0.1820.17480.16180.02750.4819-0.1250.2122-2.326226.4732-1.9939
220.522-0.0045-0.15810.33760.0540.11870.0121-0.18250.0080.1385-0.10310.1923-0.042-0.2418-0.11990.1473-0.09760.04780.32290.01450.3033-7.758426.64945.8985
230.03240.00530.02360.0287-0.03370.07810.03220.1517-0.04480.07150.14690.0105-0.0966-0.0220.09730.280.18130.16510.25940.06740.4599-8.563932.9575-8.191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 34 )
4X-RAY DIFFRACTION4chain 'A' and (resid 35 through 44 )
5X-RAY DIFFRACTION5chain 'A' and (resid 45 through 49 )
6X-RAY DIFFRACTION6chain 'A' and (resid 50 through 54 )
7X-RAY DIFFRACTION7chain 'A' and (resid 55 through 59 )
8X-RAY DIFFRACTION8chain 'A' and (resid 60 through 65 )
9X-RAY DIFFRACTION9chain 'A' and (resid 66 through 70 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 22 )
11X-RAY DIFFRACTION11chain 'B' and (resid 23 through 34 )
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 44 )
13X-RAY DIFFRACTION13chain 'B' and (resid 45 through 56 )
14X-RAY DIFFRACTION14chain 'B' and (resid 57 through 65 )
15X-RAY DIFFRACTION15chain 'B' and (resid 66 through 72 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 6 )
17X-RAY DIFFRACTION17chain 'C' and (resid 7 through 11 )
18X-RAY DIFFRACTION18chain 'C' and (resid 12 through 22 )
19X-RAY DIFFRACTION19chain 'C' and (resid 23 through 34 )
20X-RAY DIFFRACTION20chain 'C' and (resid 35 through 44 )
21X-RAY DIFFRACTION21chain 'C' and (resid 45 through 56 )
22X-RAY DIFFRACTION22chain 'C' and (resid 57 through 65 )
23X-RAY DIFFRACTION23chain 'C' and (resid 66 through 72 )

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