8RM5
Cryo-EM structure of the cross-exon pre-B+5'ssLNG+ATPyS complex
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth 66] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063442 | 3000419 | SCOP2B (2021-05-27) |
B [auth 67] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063466 | 3000419 | SCOP2B (2021-05-27) |
D [auth 63] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063456 | 3000419 | SCOP2B (2021-05-27) |
E [auth 68] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063492 | 3000419 | SCOP2B (2021-05-27) |
F [auth 64] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063488 | 3000419 | SCOP2B (2021-05-27) |
G [auth 65] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063472 | 3000419 | SCOP2B (2021-05-27) |
I [auth B4] | SCOP2B Superfamily | RNA-binding domain RBD | 8090834 | 3000110 | SCOP2B (2021-05-27) |
P [auth B3] | SCOP2B Superfamily | WD40 repeat-like | 8052534 | 3001694 | SCOP2B (2021-05-27) |
P [auth B3] | SCOP2B Superfamily | WD40 repeat-like | 8052535 | 3001694 | SCOP2B (2021-05-27) |
P [auth B3] | SCOP2B Superfamily | WD40 repeat-like | 8051197 | 3001694 | SCOP2B (2021-05-27) |
P [auth B3] | SCOP2B Superfamily | WD40 repeat-like | 8052534 | 3001694 | SCOP2B (2021-05-27) |
Q [auth BP] | SCOP2B Superfamily | Triquetra zinc finger motif | 8051848 | 3002040 | SCOP2B (2021-05-27) |
S [auth B6] | SCOP2B Superfamily | RNA-binding domain RBD | 8040695 | 3000110 | SCOP2B (2021-05-27) |
EA [auth 52] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2021-05-27) |
T [auth 22] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2021-05-27) |
NA [auth 42] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2021-05-27) |
U [auth 2B] | SCOP2B Superfamily | RNA-binding domain RBD | 8035327 | 3000110 | SCOP2B (2021-05-27) |
FA [auth 5f] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063452 | 3000419 | SCOP2B (2021-05-27) |
OA [auth 4f] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063452 | 3000419 | SCOP2B (2021-05-27) |
V [auth 2f] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063452 | 3000419 | SCOP2B (2021-05-27) |
CA [auth 5b] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041747 | 3000419 | SCOP2B (2021-05-27) |
QA [auth 4b] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041747 | 3000419 | SCOP2B (2021-05-27) |
W [auth 2b] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041747 | 3000419 | SCOP2B (2021-05-27) |
IA [auth 53] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2021-05-27) |
PA [auth 43] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2021-05-27) |
X [auth 23] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2021-05-27) |
HA [auth 5g] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2021-05-27) |
RA [auth 4g] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2021-05-27) |
Y [auth 2g] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2021-05-27) |
Z [auth 2e] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063476 | 3000419 | SCOP2B (2021-05-27) |
GA [auth 5e] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063476 | 3000419 | SCOP2B (2021-05-27) |
MA [auth 4e] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063476 | 3000419 | SCOP2B (2021-05-27) |
AA [auth 21] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2021-05-27) |
DA [auth 51] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2021-05-27) |
LA [auth 41] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2021-05-27) |
BA [auth 2A] | SCOP2B Superfamily | L domain-like | 8043993 | 3001010 | SCOP2B (2021-05-27) |
JA [auth B] | SCOP2B Superfamily | E set domains | 8055093 | 3000070 | SCOP2B (2021-05-27) |
JA [auth B] | SCOP2B Superfamily | Brl domain-like | 8036193 | 3000115 | SCOP2B (2021-05-27) |
KA [auth W] | SCOP2B Superfamily | Cyclophilin-like | 8042789 | 3000168 | SCOP2B (2021-05-27) |
WA [auth L] | SCOP2B Superfamily | Nop domain | 8033305 | 3001551 | SCOP2B (2021-05-27) |
ZA [auth A] | SCOP2B Superfamily | JAB1/MPN domain-like | 8053277 | 3001105 | SCOP2B (2021-05-27) |
ZA [auth A] | SCOP2B Superfamily | Ribonuclease H-like | 8041105 | 3000143 | SCOP2B (2021-05-27) |
CB [auth M] | SCOP2B Superfamily | L30e-like | 8043738 | 3001739 | SCOP2B (2021-05-27) |
DB [auth D] | SCOP2B Superfamily | Thioredoxin-like | 8044390 | 3000031 | SCOP2B (2021-05-27) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth 66] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
B [auth 67] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
C [auth 62] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
D [auth 63] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
E [auth 68] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
F [auth 64] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
G [auth 65] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
H [auth E] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
I [auth B4] | PF00076 | RNA recognition motif (RRM_1) | RNA recognition motif | The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ... | Domain |
K [auth 8] | PF12874 | Zinc-finger of C2H2 type (zf-met) | Zinc-finger of C2H2 type | This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding. | Domain |
K [auth 8] | PF16835 | Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) (SF3A2) | Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) | SF3A2 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp2 ... | Domain |
L [auth 9] | PF16837 | Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 (SF3A3) | Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 | SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp2 ... | Domain |
L [auth 9] | PF13297 | Replication stress response SDE2 C-terminal (SDE2_2C) | Replication stress response SDE2 C-terminal | This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved fr ... | Domain |
L [auth 9] | PF12108 | Splicing factor SF3a60 binding domain (SF3a60_bindingd) | Splicing factor SF3a60 binding domain | This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is th ... | Domain |
M [auth B2] | PF04037 | Domain of unknown function (DUF382) (DUF382) | Domain of unknown function (DUF382) | - | Family |
M [auth B2] | PF04046 | PSP (PSP) | PSP | - | Family |
P [auth B3] | PF10433 | Mono-functional DNA-alkylating methyl methanesulfonate N-term (MMS1_N) | Mono-functional DNA-alkylating methyl methanesulfonate N-term | - | Repeat |
P [auth B3] | PF03178 | CPSF A subunit region (CPSF_A) | CPSF A subunit region | - | Repeat |
R [auth B1] | PF22646 | PPP2R1A-like HEAT repeat (PPP2R1A-like_HEAT) | PPP2R1A-like HEAT repeat | - | Repeat |
S [auth B6] | PF00076 | RNA recognition motif (RRM_1) | RNA recognition motif | The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ... | Domain |
EA [auth 52], NA [auth 42], T [auth 22] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
U [auth 2B] | PF00076 | RNA recognition motif (RRM_1) | RNA recognition motif | The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ... | Domain |
U [auth 2B] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
IA [auth 53], PA [auth 43], X [auth 23] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
AA [auth 21], DA [auth 51], LA [auth 41] | PF01423 | LSM domain (LSM) | LSM domain | The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ... | Domain |
JA [auth B] | PF02889 | Sec63 Brl domain (Sec63) | Sec63 Brl domain | - | Family |
JA [auth B] | PF00270 | DEAD/DEAH box helicase (DEAD) | DEAD/DEAH box helicase | Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ... | Domain |
JA [auth B] | PF00271 | Helicase conserved C-terminal domain (Helicase_C) | Helicase conserved C-terminal domain | The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. | Domain |
KA [auth W] | PF00160 | Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase) | Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD | The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ... | Domain |
SA [auth U] | PF02148 | Zn-finger in ubiquitin-hydrolases and other protein (zf-UBP) | Zn-finger in ubiquitin-hydrolases and other protein | - | Domain |
SA [auth U] | PF00443 | Ubiquitin carboxyl-terminal hydrolase (UCH) | Ubiquitin carboxyl-terminal hydrolase | - | Family |
UA [auth G] | PF00270 | DEAD/DEAH box helicase (DEAD) | DEAD/DEAH box helicase | Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ... | Domain |
VA [auth J] | PF06544 | Small nuclear ribonucleoprotein Prp3, C-terminal domain (Prp3_C) | Small nuclear ribonucleoprotein Prp3, C-terminal domain | This domain is found at the C-terminal end of U4/U6 and U4/U5/U6- small nuclear ribonucleoprotein Prp3, part of the tri-RNA complex that form the spliceosome. Prp3 plays a key role in the recognition of the snRNA duplex. This binding domain, highly c ... | Domain |
WA [auth L] | PF09785 | Prp31 C terminal domain (Prp31_C) | Prp31 C terminal domain | - | Family |
WA [auth L] | PF01798 | snoRNA binding domain, fibrillarin (Nop) | snoRNA binding domain, fibrillarin | - | Family |
XA [auth F] | PF08799 | pre-mRNA processing factor 4 (PRP4) like (PRP4) | pre-mRNA processing factor 4 (PRP4) like | This small domain is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. | Domain |
XA [auth F] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
YA [auth N] | PF14559 | Tetratricopeptide repeat (TPR_19) | Tetratricopeptide repeat | - | Repeat |
YA [auth N] | PF06424 | PRP1 splicing factor, N-terminal (PRP1_N) | PRP1 splicing factor, N-terminal | This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing f ... | Domain |
YA [auth N] | PF13432 | Tetratricopeptide repeat (TPR_16) | Tetratricopeptide repeat | - | Repeat |
ZA [auth A] | PF10597 | U5-snRNA binding site 2 of PrP8 (U5_2-snRNA_bdg) | U5-snRNA binding site 2 of PrP8 | The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis [1]. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that ... | Domain |
ZA [auth A] | PF10598 | RNA recognition motif of the spliceosomal PrP8 (RRM_4) | RNA recognition motif of the spliceosomal PrP8 | The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is PrP8 which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molec ... | Domain |
ZA [auth A] | PF10596 | U6-snRNA interacting domain of PrP8 (U6-snRNA_bdg) | U6-snRNA interacting domain of PrP8 | This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 ... | Domain |
ZA [auth A] | PF12134 | PRP8 domain IV core (PRP8_domainIV) | PRP8 domain IV core | This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The dom ... | Domain |
ZA [auth A] | PF08082 | PRO8NT (NUC069), PrP8 N-terminal domain (PRO8NT) | PRO8NT (NUC069), PrP8 N-terminal domain | The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family [1]. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly va ... | Domain |
ZA [auth A] | PF08083 | PROCN (NUC071) domain (PROCN) | PROCN (NUC071) domain | The PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family [1]. | Domain |
ZA [auth A] | PF08084 | PROCT (NUC072) domain (PROCT) | PROCT (NUC072) domain | The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [1]. | Domain |
ZA [auth A] | PF01398 | JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB) | JAB1/Mov34/MPN/PAD-1 ubiquitin protease | - | Family |
AB [auth S] | PF03343 | SART-1 family (SART-1) | SART-1 family | - | Family |
BB [auth C] | PF00679 | Elongation factor G C-terminus (EFG_C) | Elongation factor G C-terminus | This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. | Domain |
BB [auth C] | PF00009 | Elongation factor Tu GTP binding domain (GTP_EFTU) | Elongation factor Tu GTP binding domain | This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. | Domain |
BB [auth C] | PF14492 | Elongation Factor G, domain III (EFG_III) | Elongation Factor G, domain III | This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1]. | Domain |
BB [auth C] | PF03144 | Elongation factor Tu domain 2 (GTP_EFTU_D2) | Elongation factor Tu domain 2 | Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ... | Domain |
BB [auth C] | PF03764 | Elongation factor G, domain IV (EFG_IV) | Elongation factor G, domain IV | This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. | Domain |
CB [auth M] | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae) | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ... | Domain |
DB [auth D] | PF02966 | Mitosis protein DIM1 (DIM1) | Mitosis protein DIM1 | - | Domain |
FB [auth 7] | PF01805 | Surp module (Surp) | Surp module | - | Family |
FB [auth 7] | PF12230 | Pre-mRNA splicing factor PRP21 like protein (PRP21_like_P) | Pre-mRNA splicing factor PRP21 like protein | - | Family |