8P83

Cryo-EM structure of full-length human UBR5 (homotetramer)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000209	biological_process	protein polyubiquitination
A	0000785	cellular_component	chromatin
A	0003723	molecular_function	RNA binding
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006281	biological_process	DNA repair
A	0006974	biological_process	DNA damage response
A	0008270	molecular_function	zinc ion binding
A	0010628	biological_process	positive regulation of gene expression
A	0016020	cellular_component	membrane
A	0016567	biological_process	protein ubiquitination
A	0016740	molecular_function	transferase activity
A	0032991	cellular_component	protein-containing complex
A	0033696	biological_process	heterochromatin boundary formation
A	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
A	0035519	biological_process	protein K29-linked ubiquitination
A	0042307	biological_process	positive regulation of protein import into nucleus
A	0043130	molecular_function	ubiquitin binding
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0045879	biological_process	negative regulation of smoothened signaling pathway
A	0046872	molecular_function	metal ion binding
A	0048471	cellular_component	perinuclear region of cytoplasm
A	0050847	biological_process	progesterone receptor signaling pathway
A	0061630	molecular_function	ubiquitin protein ligase activity
A	0070936	biological_process	protein K48-linked ubiquitination
A	0070979	biological_process	protein K11-linked ubiquitination
A	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
A	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
A	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
A	0140455	biological_process	cytoplasm protein quality control
A	0140861	biological_process	DNA repair-dependent chromatin remodeling
A	0141198	biological_process	protein branched polyubiquitination
B	0000209	biological_process	protein polyubiquitination
B	0000785	cellular_component	chromatin
B	0003723	molecular_function	RNA binding
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006281	biological_process	DNA repair
B	0006974	biological_process	DNA damage response
B	0008270	molecular_function	zinc ion binding
B	0010628	biological_process	positive regulation of gene expression
B	0016020	cellular_component	membrane
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0032991	cellular_component	protein-containing complex
B	0033696	biological_process	heterochromatin boundary formation
B	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
B	0035519	biological_process	protein K29-linked ubiquitination
B	0042307	biological_process	positive regulation of protein import into nucleus
B	0043130	molecular_function	ubiquitin binding
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0045879	biological_process	negative regulation of smoothened signaling pathway
B	0046872	molecular_function	metal ion binding
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0050847	biological_process	progesterone receptor signaling pathway
B	0061630	molecular_function	ubiquitin protein ligase activity
B	0070936	biological_process	protein K48-linked ubiquitination
B	0070979	biological_process	protein K11-linked ubiquitination
B	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
B	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
B	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
B	0140455	biological_process	cytoplasm protein quality control
B	0140861	biological_process	DNA repair-dependent chromatin remodeling
B	0141198	biological_process	protein branched polyubiquitination
C	0000209	biological_process	protein polyubiquitination
C	0000785	cellular_component	chromatin
C	0003723	molecular_function	RNA binding
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006281	biological_process	DNA repair
C	0006974	biological_process	DNA damage response
C	0008270	molecular_function	zinc ion binding
C	0010628	biological_process	positive regulation of gene expression
C	0016020	cellular_component	membrane
C	0016567	biological_process	protein ubiquitination
C	0016740	molecular_function	transferase activity
C	0032991	cellular_component	protein-containing complex
C	0033696	biological_process	heterochromatin boundary formation
C	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
C	0035519	biological_process	protein K29-linked ubiquitination
C	0042307	biological_process	positive regulation of protein import into nucleus
C	0043130	molecular_function	ubiquitin binding
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0045879	biological_process	negative regulation of smoothened signaling pathway
C	0046872	molecular_function	metal ion binding
C	0048471	cellular_component	perinuclear region of cytoplasm
C	0050847	biological_process	progesterone receptor signaling pathway
C	0061630	molecular_function	ubiquitin protein ligase activity
C	0070936	biological_process	protein K48-linked ubiquitination
C	0070979	biological_process	protein K11-linked ubiquitination
C	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
C	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
C	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
C	0140455	biological_process	cytoplasm protein quality control
C	0140861	biological_process	DNA repair-dependent chromatin remodeling
C	0141198	biological_process	protein branched polyubiquitination
D	0000209	biological_process	protein polyubiquitination
D	0000785	cellular_component	chromatin
D	0003723	molecular_function	RNA binding
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006281	biological_process	DNA repair
D	0006974	biological_process	DNA damage response
D	0008270	molecular_function	zinc ion binding
D	0010628	biological_process	positive regulation of gene expression
D	0016020	cellular_component	membrane
D	0016567	biological_process	protein ubiquitination
D	0016740	molecular_function	transferase activity
D	0032991	cellular_component	protein-containing complex
D	0033696	biological_process	heterochromatin boundary formation
D	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
D	0035519	biological_process	protein K29-linked ubiquitination
D	0042307	biological_process	positive regulation of protein import into nucleus
D	0043130	molecular_function	ubiquitin binding
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0045879	biological_process	negative regulation of smoothened signaling pathway
D	0046872	molecular_function	metal ion binding
D	0048471	cellular_component	perinuclear region of cytoplasm
D	0050847	biological_process	progesterone receptor signaling pathway
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0070936	biological_process	protein K48-linked ubiquitination
D	0070979	biological_process	protein K11-linked ubiquitination
D	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
D	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
D	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
D	0140455	biological_process	cytoplasm protein quality control
D	0140861	biological_process	DNA repair-dependent chromatin remodeling
D	0141198	biological_process	protein branched polyubiquitination

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	272
Details	ZN_FING: UBR-type => ECO:0000255|PROSITE-ProRule:PRU00508

Chain	Residue	Details
A	ASP1177-ALA1245
B	ASP1177-ALA1245
C	ASP1177-ALA1245
D	ASP1177-ALA1245

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	ACT_SITE: Glycyl thioester intermediate => ECO:0000255|PROSITE-ProRule:PRU00104, ECO:0000305|PubMed:11287654, ECO:0000305|PubMed:23027739, ECO:0000305|PubMed:28689657, ECO:0000305|PubMed:37040767, ECO:0000305|PubMed:37478862, ECO:0000305|PubMed:37620400

Chain	Residue	Details
A	CYS2768
B	CYS2768
C	CYS2768
D	CYS2768

---

site_id	SWS_FT_FI3
Number of Residues	44
Details	BINDING: BINDING => ECO:0000269|PubMed:37040767, ECO:0000269|PubMed:37409633, ECO:0000269|PubMed:37478846, ECO:0000269|PubMed:37620400, ECO:0007744|PDB:8BJA, ECO:0007744|PDB:8C06, ECO:0007744|PDB:8D4X, ECO:0007744|PDB:8E0Q, ECO:0007744|PDB:8EWI, ECO:0007744|PDB:8P82

Chain	Residue	Details
A	CYS1179
A	CYS1234
A	CYS1240
B	CYS1179
B	CYS1196
B	CYS1199
B	CYS1208
B	CYS1211
B	CYS1215
B	HIS1216
B	HIS1219
A	CYS1196
B	CYS1232
B	CYS1234
B	CYS1240
C	CYS1179
C	CYS1196
C	CYS1199
C	CYS1208
C	CYS1211
C	CYS1215
C	HIS1216
A	CYS1199
C	HIS1219
C	CYS1232
C	CYS1234
C	CYS1240
D	CYS1179
D	CYS1196
D	CYS1199
D	CYS1208
D	CYS1211
D	CYS1215
A	CYS1208
D	HIS1216
D	HIS1219
D	CYS1232
D	CYS1234
D	CYS1240
A	CYS1211
A	CYS1215
A	HIS1216
A	HIS1219
A	CYS1232

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N-acetylthreonine => ECO:0007744|PubMed:19413330

Chain	Residue	Details
A	THR2
B	THR2
C	THR2
D	THR2

---

site_id	SWS_FT_FI5
Number of Residues	16
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:21924388, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER110
C	SER578
C	SER612
C	SER808
D	SER110
D	SER578
D	SER612
D	SER808
A	SER578
A	SER612
A	SER808
B	SER110
B	SER578
B	SER612
B	SER808
C	SER110

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:21924388, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER327
B	SER327
C	SER327
D	SER327

---

site_id	SWS_FT_FI7
Number of Residues	56
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:21924388

Chain	Residue	Details
A	SER352
A	SER2026
A	SER2028
A	SER2076
A	SER2289
A	SER2484
B	SER352
B	SER928
B	SER1018
B	SER1227
B	SER1355
A	SER928
B	SER1375
B	SER1481
B	SER1741
B	SER1780
B	SER2026
B	SER2028
B	SER2076
B	SER2289
B	SER2484
C	SER352
A	SER1018
C	SER928
C	SER1018
C	SER1227
C	SER1355
C	SER1375
C	SER1481
C	SER1741
C	SER1780
C	SER2026
C	SER2028
A	SER1227
C	SER2076
C	SER2289
C	SER2484
D	SER352
D	SER928
D	SER1018
D	SER1227
D	SER1355
D	SER1375
D	SER1481
A	SER1355
D	SER1741
D	SER1780
D	SER2026
D	SER2028
D	SER2076
D	SER2289
D	SER2484
A	SER1375
A	SER1481
A	SER1741
A	SER1780

---

site_id	SWS_FT_FI8
Number of Residues	24
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:21924388

Chain	Residue	Details
A	THR637
B	THR1736
B	THR2030
B	THR2213
C	THR637
C	THR1115
C	THR1135
C	THR1736
C	THR2030
C	THR2213
D	THR637
A	THR1115
D	THR1115
D	THR1135
D	THR1736
D	THR2030
D	THR2213
A	THR1135
A	THR1736
A	THR2030
A	THR2213
B	THR637
B	THR1115
B	THR1135

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:21924388, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER1308
B	SER1308
C	SER1308
D	SER1308

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569

Chain	Residue	Details
A	SER1549
B	SER1549
C	SER1549
D	SER1549

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455

Chain	Residue	Details
A	TYR1746
B	TYR1746
C	TYR1746
D	TYR1746

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:21924388, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	THR1969
B	THR1969
C	THR1969
D	THR1969

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
A	SER1990
B	SER1990
C	SER1990
D	SER1990

---

site_id	SWS_FT_FI14
Number of Residues	8
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER2241
A	SER2469
B	SER2241
B	SER2469
C	SER2241
C	SER2469
D	SER2241
D	SER2469

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER2486
B	SER2486
C	SER2486
D	SER2486

---