PDB-8e7o: CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN

ID or keywords:

Entry

Database: PDB / ID: 8e7o

Title

CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN

Components

(Ubiquitin) x 2

Keywords

SIGNALING PROTEIN / Degradation / Polypeptide / Homeostasis / Post-translational modification / Polyubiquitin chain

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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Lemma, B.E. / Fushman, D.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation.
Authors: Lemma, B. / Zhang, D. / Vamisetti, G.B. / Wentz, B.G. / Suga, H. / Brik, A. / Lubkowski, J. / Fushman, D.

History

Deposition	Aug 24, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	Nov 15, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8e7o.cif.gz	183 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8e7o_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
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Related structure data

Related structure data	8f1fC 1aarS S: Starting model for refinement C: citing same article (ref.)
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) #255 - Mar 2021 Cisplatin and DNA similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (2) #195 - Mar 2016 RAF Protein Kinases similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

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Related items in Molecule of the Month

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

Deposited unit

A: Ubiquitin

B: Ubiquitin

C: Ubiquitin

D: Ubiquitin

hetero molecules

34.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	58.839, 77.164, 135.823
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 76 / Label seq-ID: 1 - 76

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Ubiquitin 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: Protein	Ubiquitin Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K48R 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
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.21 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 25% w/v PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.7→67.911 Å / Num. obs: 34404 / % possible obs: 99.3 % / Redundancy: 7.8 % / CC_1/2: 1 / Net I/σ(I): 1.27
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 7.3 % / Num. unique obs: 1754 / CC_1/2: 0.355 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
DIALS		data reduction
Aimless		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AAR

1aar

Resolution: 1.7→67.911 Å / Cor.coef. F_o:F_c: 0.982 / Cor.coef. F_o:F_c free: 0.965 / WR_factor R_free: 0.22 / WR_factor R_work: 0.151 / SU B: 9.038 / SU ML: 0.117 / Average fsc free: 0.9433 / Average fsc work: 0.9616 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.108 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2206	1742	5.098 %
R_work	0.1567	32425	-
all	0.16	-	-
obs	-	34167	99.265 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.053 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.61 Å²	-0 Å²	0 Å²
2-	-	0.338 Å²	-0 Å²
3-	-	-	0.272 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→67.911 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2406	0	20	160	2586

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2449
X-RAY DIFFRACTION	r_angle_refined_deg	2.19	1.655	3291
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.284	5	300
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.656	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.336	10	495
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.038	10	109
X-RAY DIFFRACTION	r_chiral_restr	0.153	0.2	392
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1732
X-RAY DIFFRACTION	r_nbd_refined	0.148	0.2	981
X-RAY DIFFRACTION	r_nbtor_refined	0.253	0.2	1572
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	164
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.16	0.2	111
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.224	0.2	50
X-RAY DIFFRACTION	r_mcbond_it	7.721	4.305	1212
X-RAY DIFFRACTION	r_mcangle_it	8.025	6.457	1508
X-RAY DIFFRACTION	r_scbond_it	15.47	5.278	1237
X-RAY DIFFRACTION	r_scangle_it	15.869	7.564	1783
X-RAY DIFFRACTION	r_lrange_it	14.088	109.971	3543
X-RAY DIFFRACTION	r_rigid_bond_restr	7.753	3	2449
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.145	0.05	2082
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.104	0.05	2203
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.128	0.05	2122
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.135	0.05	2124
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.143	0.05	2096
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.129	0.05	2143

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.14492	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.14492	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.1044	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.1044	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.12817	0.05007
3	6	A	X-RAY DIFFRACTION	Local ncs	0.12817	0.05007
4	7	A	X-RAY DIFFRACTION	Local ncs	0.13517	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.13517	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.14295	0.05007
5	10	A	X-RAY DIFFRACTION	Local ncs	0.14295	0.05007
6	11	A	X-RAY DIFFRACTION	Local ncs	0.12889	0.05007
6	12	A	X-RAY DIFFRACTION	Local ncs	0.12889	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.7-1.744	0.415	129	0.417	2258	0.417	2505	0.831	0.839	95.2894	0.377
1.744-1.792	0.385	126	0.372	2304	0.373	2457	0.887	0.89	98.9011	0.328
1.792-1.844	0.323	112	0.31	2269	0.311	2381	0.922	0.925	100	0.258
1.844-1.901	0.336	105	0.251	2186	0.255	2298	0.924	0.955	99.6954	0.198
1.901-1.963	0.27	114	0.194	2137	0.198	2263	0.952	0.973	99.4697	0.142
1.963-2.032	0.271	118	0.177	2040	0.183	2204	0.955	0.98	97.9129	0.136
2.032-2.108	0.26	104	0.158	1981	0.163	2085	0.96	0.984	100	0.121
2.108-2.194	0.253	94	0.159	1918	0.164	2013	0.959	0.984	99.9503	0.125
2.194-2.292	0.231	104	0.148	1848	0.153	1955	0.966	0.986	99.8465	0.117
2.292-2.403	0.223	97	0.124	1754	0.129	1854	0.968	0.991	99.8382	0.098
2.403-2.533	0.244	101	0.133	1675	0.139	1776	0.964	0.989	100	0.112
2.533-2.687	0.233	71	0.143	1621	0.147	1694	0.968	0.987	99.8819	0.122
2.687-2.872	0.334	70	0.167	1494	0.174	1581	0.935	0.983	98.9247	0.151
2.872-3.101	0.227	83	0.161	1390	0.165	1474	0.967	0.984	99.9322	0.154
3.101-3.397	0.247	61	0.163	1308	0.167	1369	0.961	0.983	100	0.167
3.397-3.797	0.207	76	0.144	1166	0.148	1243	0.975	0.987	99.9195	0.155
3.797-4.382	0.17	69	0.123	1046	0.125	1119	0.983	0.991	99.6425	0.139
4.382-5.361	0.168	48	0.122	899	0.124	950	0.984	0.992	99.6842	0.143
5.361-7.558	0.244	32	0.166	703	0.169	741	0.977	0.981	99.1903	0.192
7.558-67.911	0.11	27	0.147	425	0.145	452	0.989	0.981	100	0.197

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