8QPE

Cryo-EM Structure of Pre-B-like Complex (core part)

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
7	0000389	biological_process	mRNA 3'-splice site recognition
7	0000398	biological_process	mRNA splicing, via spliceosome
7	0003723	molecular_function	RNA binding
7	0005515	molecular_function	protein binding
7	0005634	cellular_component	nucleus
7	0005654	cellular_component	nucleoplasm
7	0005681	cellular_component	spliceosomal complex
7	0005684	cellular_component	U2-type spliceosomal complex
7	0005686	cellular_component	U2 snRNP
7	0006397	biological_process	mRNA processing
7	0008380	biological_process	RNA splicing
7	0016607	cellular_component	nuclear speck
7	0071004	cellular_component	U2-type prespliceosome
7	0071005	cellular_component	U2-type precatalytic spliceosome
7	0071013	cellular_component	catalytic step 2 spliceosome
7	1903241	biological_process	U2-type prespliceosome assembly
A	0000244	biological_process	spliceosomal tri-snRNP complex assembly
A	0000375	biological_process	RNA splicing, via transesterification reactions
A	0000398	biological_process	mRNA splicing, via spliceosome
A	0003723	molecular_function	RNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005681	cellular_component	spliceosomal complex
A	0005682	cellular_component	U5 snRNP
A	0006397	biological_process	mRNA processing
A	0008233	molecular_function	peptidase activity
A	0008380	biological_process	RNA splicing
A	0016020	cellular_component	membrane
A	0016607	cellular_component	nuclear speck
A	0017070	molecular_function	U6 snRNA binding
A	0030532	cellular_component	small nuclear ribonucleoprotein complex
A	0030619	molecular_function	U1 snRNA binding
A	0030620	molecular_function	U2 snRNA binding
A	0030623	molecular_function	U5 snRNA binding
A	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
A	0070530	molecular_function	K63-linked polyubiquitin modification-dependent protein binding
A	0071005	cellular_component	U2-type precatalytic spliceosome
A	0071006	cellular_component	U2-type catalytic step 1 spliceosome
A	0071007	cellular_component	U2-type catalytic step 2 spliceosome
A	0071013	cellular_component	catalytic step 2 spliceosome
A	0071222	biological_process	cellular response to lipopolysaccharide
A	0071356	biological_process	cellular response to tumor necrosis factor
A	0097157	molecular_function	pre-mRNA intronic binding
A	0140492	molecular_function	metal-dependent deubiquitinase activity
C	0000398	biological_process	mRNA splicing, via spliceosome
C	0003723	molecular_function	RNA binding
C	0003924	molecular_function	GTPase activity
C	0005515	molecular_function	protein binding
C	0005525	molecular_function	GTP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005681	cellular_component	spliceosomal complex
C	0005829	cellular_component	cytosol
C	0006397	biological_process	mRNA processing
C	0008380	biological_process	RNA splicing
C	0015030	cellular_component	Cajal body
C	0016020	cellular_component	membrane
C	0016607	cellular_component	nuclear speck
C	0030623	molecular_function	U5 snRNA binding
C	0042220	biological_process	response to cocaine
C	0043231	cellular_component	intracellular membrane-bounded organelle
C	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
C	0071005	cellular_component	U2-type precatalytic spliceosome
C	0071007	cellular_component	U2-type catalytic step 2 spliceosome
C	0071013	cellular_component	catalytic step 2 spliceosome
C	0071466	biological_process	cellular response to xenobiotic stimulus
D	0000245	biological_process	spliceosomal complex assembly
D	0000375	biological_process	RNA splicing, via transesterification reactions
D	0000398	biological_process	mRNA splicing, via spliceosome
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005681	cellular_component	spliceosomal complex
D	0005682	cellular_component	U5 snRNP
D	0005829	cellular_component	cytosol
D	0006397	biological_process	mRNA processing
D	0008380	biological_process	RNA splicing
D	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
D	0051301	biological_process	cell division
D	0071005	cellular_component	U2-type precatalytic spliceosome
F	0000375	biological_process	RNA splicing, via transesterification reactions
F	0000398	biological_process	mRNA splicing, via spliceosome
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005681	cellular_component	spliceosomal complex
F	0006396	biological_process	RNA processing
F	0006397	biological_process	mRNA processing
F	0008380	biological_process	RNA splicing
F	0015030	cellular_component	Cajal body
F	0016607	cellular_component	nuclear speck
F	0017070	molecular_function	U6 snRNA binding
F	0030621	molecular_function	U4 snRNA binding
F	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
F	0071001	cellular_component	U4/U6 snRNP
F	0071005	cellular_component	U2-type precatalytic spliceosome
F	0097525	cellular_component	spliceosomal snRNP complex
I	0000398	biological_process	mRNA splicing, via spliceosome
I	0003723	molecular_function	RNA binding
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005681	cellular_component	spliceosomal complex
I	0006397	biological_process	mRNA processing
I	0008380	biological_process	RNA splicing
I	0071005	cellular_component	U2-type precatalytic spliceosome
I	0071011	cellular_component	precatalytic spliceosome
J	0000244	biological_process	spliceosomal tri-snRNP complex assembly
J	0000375	biological_process	RNA splicing, via transesterification reactions
J	0000398	biological_process	mRNA splicing, via spliceosome
J	0003723	molecular_function	RNA binding
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005681	cellular_component	spliceosomal complex
J	0005829	cellular_component	cytosol
J	0006397	biological_process	mRNA processing
J	0008380	biological_process	RNA splicing
J	0015030	cellular_component	Cajal body
J	0016607	cellular_component	nuclear speck
J	0032991	cellular_component	protein-containing complex
J	0042802	molecular_function	identical protein binding
J	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
J	0071005	cellular_component	U2-type precatalytic spliceosome
K	0000398	biological_process	mRNA splicing, via spliceosome
K	0001527	cellular_component	microfibril
K	0003723	molecular_function	RNA binding
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005681	cellular_component	spliceosomal complex
K	0005684	cellular_component	U2-type spliceosomal complex
K	0005813	cellular_component	centrosome
K	0006397	biological_process	mRNA processing
K	0008380	biological_process	RNA splicing
K	0071005	cellular_component	U2-type precatalytic spliceosome
L	0000244	biological_process	spliceosomal tri-snRNP complex assembly
L	0000398	biological_process	mRNA splicing, via spliceosome
L	0003723	molecular_function	RNA binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005681	cellular_component	spliceosomal complex
L	0005684	cellular_component	U2-type spliceosomal complex
L	0005687	cellular_component	U4 snRNP
L	0005690	cellular_component	U4atac snRNP
L	0006397	biological_process	mRNA processing
L	0008380	biological_process	RNA splicing
L	0015030	cellular_component	Cajal body
L	0016607	cellular_component	nuclear speck
L	0030621	molecular_function	U4 snRNA binding
L	0030622	molecular_function	U4atac snRNA binding
L	0030674	molecular_function	protein-macromolecule adaptor activity
L	0042802	molecular_function	identical protein binding
L	0043021	molecular_function	ribonucleoprotein complex binding
L	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
L	0048254	biological_process	snoRNA localization
L	0070990	molecular_function	snRNP binding
L	0071005	cellular_component	U2-type precatalytic spliceosome
L	0071011	cellular_component	precatalytic spliceosome
L	0071166	biological_process	ribonucleoprotein complex localization
L	0071339	cellular_component	MLL1 complex
L	0097526	cellular_component	spliceosomal tri-snRNP complex
M	0000398	biological_process	mRNA splicing, via spliceosome
M	0000492	biological_process	box C/D snoRNP assembly
M	0001651	cellular_component	dense fibrillar component
M	0003723	molecular_function	RNA binding
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005681	cellular_component	spliceosomal complex
M	0005690	cellular_component	U4atac snRNP
M	0005730	cellular_component	nucleolus
M	0006397	biological_process	mRNA processing
M	0007338	biological_process	single fertilization
M	0008380	biological_process	RNA splicing
M	0030490	biological_process	maturation of SSU-rRNA
M	0030515	molecular_function	snoRNA binding
M	0030621	molecular_function	U4 snRNA binding
M	0030622	molecular_function	U4atac snRNA binding
M	0031428	cellular_component	box C/D methylation guide snoRNP complex
M	0032040	cellular_component	small-subunit processome
M	0032991	cellular_component	protein-containing complex
M	0034511	molecular_function	U3 snoRNA binding
M	0034512	molecular_function	box C/D sno(s)RNA binding
M	0042274	biological_process	ribosomal small subunit biogenesis
M	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
M	0051117	molecular_function	ATPase binding
M	0071005	cellular_component	U2-type precatalytic spliceosome
M	0071011	cellular_component	precatalytic spliceosome
N	0000244	biological_process	spliceosomal tri-snRNP complex assembly
N	0000245	biological_process	spliceosomal complex assembly
N	0000375	biological_process	RNA splicing, via transesterification reactions
N	0000398	biological_process	mRNA splicing, via spliceosome
N	0003723	molecular_function	RNA binding
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005681	cellular_component	spliceosomal complex
N	0005682	cellular_component	U5 snRNP
N	0006397	biological_process	mRNA processing
N	0006403	biological_process	RNA localization
N	0008380	biological_process	RNA splicing
N	0016020	cellular_component	membrane
N	0016607	cellular_component	nuclear speck
N	0030674	molecular_function	protein-macromolecule adaptor activity
N	0042802	molecular_function	identical protein binding
N	0043021	molecular_function	ribonucleoprotein complex binding
N	0045944	biological_process	positive regulation of transcription by RNA polymerase II
N	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
N	0071005	cellular_component	U2-type precatalytic spliceosome
N	0071013	cellular_component	catalytic step 2 spliceosome
r	0000398	biological_process	mRNA splicing, via spliceosome
r	0003677	molecular_function	DNA binding
r	0005515	molecular_function	protein binding
r	0005634	cellular_component	nucleus
r	0005654	cellular_component	nucleoplasm
r	0005681	cellular_component	spliceosomal complex
r	0006397	biological_process	mRNA processing
r	0008380	biological_process	RNA splicing
r	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
r	0046872	molecular_function	metal ion binding
r	0071005	cellular_component	U2-type precatalytic spliceosome
S	0000387	biological_process	spliceosomal snRNP assembly
S	0000398	biological_process	mRNA splicing, via spliceosome
S	0000481	biological_process	maturation of 5S rRNA
S	0003723	molecular_function	RNA binding
S	0005515	molecular_function	protein binding
S	0005634	cellular_component	nucleus
S	0005654	cellular_component	nucleoplasm
S	0005681	cellular_component	spliceosomal complex
S	0005737	cellular_component	cytoplasm
S	0005794	cellular_component	Golgi apparatus
S	0005829	cellular_component	cytosol
S	0006397	biological_process	mRNA processing
S	0008380	biological_process	RNA splicing
S	0015030	cellular_component	Cajal body
S	0016607	cellular_component	nuclear speck
S	0045292	biological_process	mRNA cis splicing, via spliceosome
S	0045585	biological_process	positive regulation of cytotoxic T cell differentiation
S	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
S	0071005	cellular_component	U2-type precatalytic spliceosome
S	0071013	cellular_component	catalytic step 2 spliceosome
U	0000245	biological_process	spliceosomal complex assembly
U	0000398	biological_process	mRNA splicing, via spliceosome
U	0004843	molecular_function	cysteine-type deubiquitinase activity
U	0005515	molecular_function	protein binding
U	0005634	cellular_component	nucleus
U	0005654	cellular_component	nucleoplasm
U	0005681	cellular_component	spliceosomal complex
U	0006397	biological_process	mRNA processing
U	0008380	biological_process	RNA splicing
U	0016787	molecular_function	hydrolase activity
U	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
U	0046872	molecular_function	metal ion binding
U	0051301	biological_process	cell division
X	0000398	biological_process	mRNA splicing, via spliceosome
X	0003723	molecular_function	RNA binding
X	0005515	molecular_function	protein binding
X	0005634	cellular_component	nucleus
X	0005654	cellular_component	nucleoplasm
X	0005681	cellular_component	spliceosomal complex
X	0006397	biological_process	mRNA processing
X	0008380	biological_process	RNA splicing
X	0016607	cellular_component	nuclear speck
X	0045292	biological_process	mRNA cis splicing, via spliceosome
X	0046872	molecular_function	metal ion binding
X	0070064	molecular_function	proline-rich region binding
X	0071005	cellular_component	U2-type precatalytic spliceosome
X	0071011	cellular_component	precatalytic spliceosome

Functional Information from PROSITE/UniProt

site_id	PS00028
Number of Residues	23
Details	ZINC_FINGER_C2H2_1 Zinc finger C2H2 type domain signature. Cnv..CdcvVkdsinfldHingkkH

Chain	Residue	Details
r	CYS82-HIS104

---

site_id	PS00436
Number of Residues	12
Details	PEROXIDASE_2 Peroxidases active site signature. TVrvARVmWHPS

Chain	Residue	Details
F	THR323-SER334

---

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. LGTTcyDrSWRLWDL

Chain	Residue	Details
F	LEU338-LEU352
F	ILE422-LEU436

---

site_id	PS01082
Number of Residues	18
Details	RIBOSOMAL_L7AE Ribosomal protein L7Ae signature. CedknVPYvfVrSKqaLG

Chain	Residue	Details
M	CYS73-GLY90

---

site_id	PS01159
Number of Residues	26
Details	WW_DOMAIN_1 WW/rsp5/WWP domain signature. WvegitsegyhyYYdlisga.SQWEKP

Chain	Residue	Details
X	TRP128-PRO153
X	TRP169-PRO194

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	SITE: Interaction with U4 snRNA and U4atac snRNA => ECO:0000269|PubMed:17412961, ECO:0000269|PubMed:21784869

Chain	Residue	Details
M	GLU61
M	LYS86
C	ASN258

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:19413330

Chain	Residue	Details
M	MET1
I	SER194
S	SER761
S	SER789

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: N-acetylthreonine; in NHP2-like protein 1, N-terminally processed => ECO:0000269|Ref.7, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:25944712

Chain	Residue	Details
M	THR2
X	SER229
r	LYS36
r	LYS39
r	LYS55
r	LYS61
r	LYS70
r	LYS102
r	LYS123

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9D0T1

Chain	Residue	Details
M	LYS21
K	SER361
K	SER432
J	LYS252

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
M	SER122

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:17487921, ECO:0007744|PubMed:18318008, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569

Chain	Residue	Details
K	SER118
S	SER621

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
K	SER132

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
K	SER133
7	TYR759
S	SER598

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:17487921, ECO:0007744|PubMed:18318008, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569

Chain	Residue	Details
K	THR267

---

site_id	SWS_FT_FI10
Number of Residues	7
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
K	LYS67
7	LYS131
K	LYS357
K	LYS371
K	LYS381
K	LYS415
K	LYS418

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733

Chain	Residue	Details
K	LYS249
7	LYS686
L	LYS478

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:28112733

Chain	Residue	Details
7	LYS542
S	LYS648
S	LYS657
S	LYS684
S	LYS699
S	LYS709
S	LYS723
S	LYS749
S	LYS758
S	LYS775
S	LYS780
S	LYS791
S	LYS133
S	LYS277
S	LYS329
S	LYS336
S	LYS400
S	LYS414
S	LYS548

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25114211, ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733

Chain	Residue	Details
S	LYS141

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733

Chain	Residue	Details
S	LYS147
S	LYS188

---