PDB-9ovx: CRYSTAL STRUCTURE OF UBIQUITIN K27M MUTANT

ID or keywords:

Entry

Database: PDB / ID: 9ovx

Title

CRYSTAL STRUCTURE OF UBIQUITIN K27M MUTANT

Components

Ubiquitin

Keywords

SIGNALING PROTEIN / protein degradation / protein modification / proteasome-targeting / proteolytic pathway / PROTEIN TRANSPORT

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 / 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 ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / 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 / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / 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 / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Ubiquitin-dependent degradation of Cyclin D / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Stabilization of p53 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis / Assembly of the pre-replicative complex / EGFR downregulation / Vpu mediated degradation of CD4 / Regulation of TNFR1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Assembly Of The HIV Virion / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / Spry regulation of FGF signaling / Late endosomal microautophagy / Hh mutants are degraded by ERAD / Iron uptake and transport / Activation of NF-kappaB in B cells / NOD1/2 Signaling Pathway / G2/M Checkpoints
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.5 Å

Authors

Lubkowski, J. / Wentz, B.G. / Fushman, D. / Gardiner, C.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The impact of Lysine-27 mutation on ubiquitin structure, dynamics, and receptor recognition
Authors: Gardiner, C. / Wentz, B.G. / Lubkowski, J. / Fushman, D.

History

Deposition	Jun 1, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 15, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ovx.cif.gz	50.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9ovx.ent.gz	36.5 KB	Display	PDB format
PDBx/mmJSON format	9ovx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/9ovx ftp://data.pdbj.org/pub/pdb/validation_reports/ov/9ovx	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (67) #234 - Jun 2019 MDM2 and Cancer similarity (66) #122 - Feb 2010 Enhanceosome similarity (6) #88 - Apr 2007 Clathrin similarity (1) #150 - Jun 2012 Sliding Clamps similarity (5) #172 - Apr 2014 RecA and Rad51 similarity (8) #68 - Aug 2005 Neurotrophins similarity (3) #143 - Nov 2011 Toll-like Receptors similarity (4) #56 - Aug 2004 Caspases similarity (3) #43 - Jul 2003 Src Tyrosine Kinase similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (2) #163 - Jul 2013 HIV Capsid similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#60 - Dec 2004
Ubiquitin
similarity (67)
#234 - Jun 2019
MDM2 and Cancer
similarity (66)
#122 - Feb 2010
Enhanceosome
similarity (6)
#88 - Apr 2007
Clathrin
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (5)
#172 - Apr 2014
RecA and Rad51
similarity (8)
#68 - Aug 2005
Neurotrophins
similarity (3)
#143 - Nov 2011
Toll-like Receptors
similarity (4)
#56 - Aug 2004
Caspases
similarity (3)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (2)
#126 - Jun 2010
Epidermal Growth Factor
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (2)
#163 - Jul 2013
HIV Capsid
similarity (1)
#195 - Mar 2016
RAF Protein Kinases
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)

Deposited unit

A: Ubiquitin

hetero molecules

9.47 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: homology

Unit cell

Length a, b, c (Å)	144.574, 144.574, 144.574
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	209
Space group name H-M	F432

Components on special symmetry positions

ID	Model	Components
1	1	A-101- CD
2	1	A-105- CD
3	1	A-245- HOH
4	1	A-258- HOH
5	1	A-269- HOH

#1: Protein	Ubiquitin Mass: 8578.847 Da / Num. of mol.: 1 / Mutation: K27M Source method: isolated from a genetically manipulated source Details: Differs from wild type ubiquitin by the mutation Lys -> Met in position 27. Last four residues were disordered in the crystal structure. Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48
#2: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.95 Å³/Da / Density % sol: 68.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: CdCl2 (0.2 M), PEG400 (10% v/v), 2-methyl-2,4-pentanediol (12% v/v) and sodium acetate buffer (0.1 M, pH 4.6) PH range: 4.6-7.3

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 19-ID / Wavelength: 0.97857 Å

Detector

Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 3, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 1.5→40 Å / Num. obs: 21257 / % possible obs: 99.6 % / Redundancy: 9.5 % / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.022 / R_rim(I) all: 0.069 / Χ²: 0.876 / Net I/σ(I): 10.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.5-1.53	5.1	0.756	1022	0.667	0.894	0.374	0.848	0.728	97.7
1.53-1.55	6.2	0.656	1022	0.746	0.924	0.287	0.719	0.731	98.1
1.55-1.58	7.6	0.593	1010	0.827	0.952	0.231	0.638	0.745	99
1.58-1.62	9	0.471	1046	0.922	0.979	0.167	0.5	0.782	99.8
1.62-1.65	10.2	0.434	1045	0.943	0.985	0.142	0.458	0.81	100
1.65-1.69	10.6	0.337	1039	0.97	0.992	0.108	0.354	0.852	99.9
1.69-1.73	10.5	0.273	1042	0.978	0.994	0.088	0.287	0.905	100
1.73-1.78	10.6	0.23	1031	0.979	0.995	0.074	0.241	0.929	100
1.78-1.83	10.4	0.179	1070	0.98	0.995	0.058	0.188	0.956	99.9
1.83-1.89	10.3	0.148	1052	0.992	0.998	0.048	0.156	0.929	100
1.89-1.96	10.2	0.121	1045	0.991	0.998	0.04	0.127	0.947	100
1.96-2.04	10	0.097	1058	0.995	0.999	0.032	0.103	0.978	100
2.04-2.13	9.2	0.08	1075	0.996	0.999	0.028	0.085	0.891	100
2.13-2.24	9.3	0.07	1033	0.996	0.999	0.024	0.074	0.878	99.2
2.24-2.38	10.4	0.064	1076	0.998	0.999	0.021	0.068	0.903	100
2.38-2.56	10.6	0.059	1076	0.997	0.999	0.019	0.062	0.93	100
2.56-2.82	10.4	0.053	1080	0.998	1	0.017	0.056	0.909	100
2.82-3.23	10.1	0.049	1099	0.997	0.999	0.016	0.052	0.942	99.9
3.23-4.07	8.8	0.048	1114	0.998	0.999	0.017	0.051	0.955	100
4.07-40	9.4	0.037	1222	0.997	0.999	0.013	0.04	0.635	99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-3000		data scaling
HKL-3000		data reduction
AutoSol		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.5→33.19 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.971 / SU B: 1.538 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.15367	1064	5.1 %	RANDOM
R_work	0.12855	-	-	-
obs	0.12979	19817	97.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.001 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: 1 / Resolution: 1.5→33.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	573	0	12	75	660

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.013	598
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	586
X-RAY DIFFRACTION	r_angle_refined_deg	2.115	1.658	806
X-RAY DIFFRACTION	r_angle_other_deg	1.574	1.583	1373
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.23	5	73
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.932	23.939	33
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.735	15	126
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.875	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	84
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	643
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	105
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.091	1.902	289
X-RAY DIFFRACTION	r_mcbond_other	2.766	1.888	288
X-RAY DIFFRACTION	r_mcangle_it	3.75	2.866	360
X-RAY DIFFRACTION	r_mcangle_other	3.813	2.875	361
X-RAY DIFFRACTION	r_scbond_it	6.688	2.684	309
X-RAY DIFFRACTION	r_scbond_other	6.678	2.685	310
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.676	3.717	446
X-RAY DIFFRACTION	r_long_range_B_refined	6.554	26.197	662
X-RAY DIFFRACTION	r_long_range_B_other	6.218	24.557	636
X-RAY DIFFRACTION	r_rigid_bond_restr	6.039	3	1184
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.267	69	-
R_work	0.229	1121	-
obs	-	-	78.55 %

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