7VPX
The cryo-EM structure of the human pre-A complex
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
M [auth F] | SCOP2B Superfamily | L domain-like | 8043993 | 3001010 | SCOP2B (2022-06-29) |
N [auth G] | SCOP2B Superfamily | RNA-binding domain RBD | 8035327 | 3000110 | SCOP2B (2022-06-29) |
FA [auth i] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2022-06-29) |
O [auth a] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041749 | 3000419 | SCOP2B (2022-06-29) |
P [auth b] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063452 | 3000419 | SCOP2B (2022-06-29) |
Z [auth m] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063452 | 3000419 | SCOP2B (2022-06-29) |
EA [auth l] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063476 | 3000419 | SCOP2B (2022-06-29) |
Q [auth c] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063476 | 3000419 | SCOP2B (2022-06-29) |
DA [auth n] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2022-06-29) |
R [auth d] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8063468 | 3000419 | SCOP2B (2022-06-29) |
HA [auth j] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2022-06-29) |
S [auth e] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041751 | 3000419 | SCOP2B (2022-06-29) |
BA [auth k] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041747 | 3000419 | SCOP2B (2022-06-29) |
T [auth f] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041747 | 3000419 | SCOP2B (2022-06-29) |
AA [auth h] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2022-06-29) |
U [auth g] | SCOP2B Superfamily | Sm-like ribonucleoproteins | 8041748 | 3000419 | SCOP2B (2022-06-29) |
Y [auth O] | SCOP2B Superfamily | RNA-binding domain RBD | 8088186 | 3000110 | SCOP2B (2022-06-29) |
CA [auth M] | SCOP2B Superfamily | RNA-binding domain RBD | 8043930 | 3000110 | SCOP2B (2022-06-29) |
GA [auth N] | SCOP2B Superfamily | beta-beta-alpha zinc fingers | 8037719 | 3001077 | SCOP2B (2022-06-29) |
IA [auth 6] | SCOP2B Superfamily | Triquetra zinc finger motif | 8051848 | 3002040 | SCOP2B (2022-06-29) |
G [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8052535 | 3001694 | SCOP2B (2022-06-29) |
G [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8052534 | 3001694 | SCOP2B (2022-06-29) |
G [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8051197 | 3001694 | SCOP2B (2022-06-29) |
G [auth 3] | SCOP2B Superfamily | WD40 repeat-like | 8052534 | 3001694 | SCOP2B (2022-06-29) |
H [auth 4] | SCOP2B Superfamily | RNA-binding domain RBD | 8090834 | 3000110 | SCOP2B (2022-06-29) |
H [auth 4] | SCOP2B Superfamily | RNA-binding domain RBD | 8033620 | 3000110 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth B] | PF16835 | e7vpxB2 | A: beta sandwiches | X: HSP20-like | H: Pre-mRNA-splicing factor PRP11 C-terminal domain (From Topology) | T: Pre-mRNA-splicing factor PRP11 C-terminal domain | F: PF16835 | ECOD (1.6) |
A [auth B] | PF12874 | e7vpxB1 | A: few secondary structure elements | X: beta-beta-alpha zinc fingers | H: beta-beta-alpha zinc fingers (From Topology) | T: beta-beta-alpha zinc fingers | F: PF12874 | ECOD (1.6) |
J [auth A] | PF01805,PF12230 | e7vpxA1 | A: alpha bundles | X: Surp module (SWAP domain) (From Topology) | H: Surp module (SWAP domain) (From Topology) | T: Surp module (SWAP domain) | F: PF01805,PF12230 | ECOD (1.6) |
M [auth F] | PF14580 | e7vpxF1 | A: beta duplicates or obligate multimers | X: Single-stranded right-handed beta-helix | H: Leucine-rich repeats (From Topology) | T: Leucine-rich repeats | F: PF14580 | ECOD (1.6) |
N [auth G] | PF00076 | e7vpxG2 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: PF00076 | ECOD (1.6) |
FA [auth i] | PF01423 | e7vpxi1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
O [auth a] | PF01423 | e7vpxa1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
P [auth b] | PF01423 | e7vpxb1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
Z [auth m] | PF01423 | e7vpxm1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
EA [auth l] | PF01423 | e7vpxl1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
Q [auth c] | PF01423 | e7vpxc1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
DA [auth n] | PF01423 | e7vpxn1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
R [auth d] | PF01423 | e7vpxd1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
HA [auth j] | PF01423 | e7vpxj1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
S [auth e] | PF01423 | e7vpxe1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
B [auth D] | PF00013 | e7vpxD1 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: KH-domains | T: Eukaryotic type KH-domain (KH-domain type I) | F: PF00013 | ECOD (1.6) |
B [auth D] | PF16275 | e7vpxD2 | A: extended segments | X: Splicing factor 1 N-terminal domain (From Topology) | H: Splicing factor 1 N-terminal domain (From Topology) | T: Splicing factor 1 N-terminal domain | F: PF16275 | ECOD (1.6) |
BA [auth k] | PF01423 | e7vpxk1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
T [auth f] | PF01423 | e7vpxf1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
AA [auth h] | PF01423 | e7vpxh1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
U [auth g] | PF01423 | e7vpxg1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01423 | ECOD (1.6) |
CA [auth M] | PF00076 | e7vpxM1 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: PF00076 | ECOD (1.6) |
GA [auth N] | PF06220 | e7vpxN1 | A: few secondary structure elements | X: beta-beta-alpha zinc fingers | H: beta-beta-alpha zinc fingers (From Topology) | T: beta-beta-alpha zinc fingers | F: PF06220 | ECOD (1.6) |
IA [auth 6] | PF03660 | e7vpx61 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: PHD finger-like domain-containing protein 5A | F: PF03660 | ECOD (1.6) |
E [auth 1] | PF22646 | e7vpx11 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: PF22646 | ECOD (1.6) |
G [auth 3] | PF03178,PF10433 | e7vpx31 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: PF03178,PF10433 | ECOD (1.6) |
G [auth 3] | PF10433 | e7vpx34 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: PF10433 | ECOD (1.6) |
G [auth 3] | PF03178 | e7vpx32 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: PF03178 | ECOD (1.6) |
H [auth 4] | PF00076 | e7vpx42 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: PF00076 | ECOD (1.6) |
I [auth 5] | PF07189 | e7vpx51 | A: alpha arrays | X: RDS3 complex subunit 10 (From Topology) | H: RDS3 complex subunit 10 (From Topology) | T: RDS3 complex subunit 10 | F: PF07189 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth B] | 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 |
A [auth B] | 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 |
J [auth A] | PF12230 | Pre-mRNA splicing factor PRP21 like protein (PRP21_like_P) | Pre-mRNA splicing factor PRP21 like protein | - | Family |
J [auth A] | PF01805 | Surp module (Surp) | Surp module | - | Family |
K [auth C] | 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 |
K [auth C] | 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 |
K [auth C] | 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 |
L [auth E] | 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 |
L [auth E] | 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 |
M [auth F] | PF14580 | Leucine-rich repeat (LRR_9) | Leucine-rich repeat | - | Repeat |
N [auth G] | 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 |
FA [auth i], O [auth a] | 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 |
P [auth b], Z [auth m] | 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 |
EA [auth l], Q [auth c] | 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 |
DA [auth n], R [auth d] | 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 |
HA [auth j], S [auth e] | 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 D] | PF00013 | KH domain (KH_1) | KH domain | KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. | Domain |
BA [auth k], T [auth f] | 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 h], U [auth g] | 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 |
Y [auth O] | PF12220 | U1 small nuclear ribonucleoprotein of 70kDa MW N terminal (U1snRNP70_N) | U1 small nuclear ribonucleoprotein of 70kDa MW N terminal | - | Family |
Y [auth O] | 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 |
CA [auth M] | 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 |
GA [auth N] | PF06220 | U1 zinc finger (zf-U1) | U1 zinc finger | This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class o ... | Domain |
IA [auth 6] | PF03660 | PHF5-like protein (PHF5) | PHF5-like protein | - | Family |
F [auth 2] | PF04037 | Domain of unknown function (DUF382) (DUF382) | Domain of unknown function (DUF382) | - | Family |
G [auth 3] | PF10433 | Mono-functional DNA-alkylating methyl methanesulfonate N-term (MMS1_N) | Mono-functional DNA-alkylating methyl methanesulfonate N-term | - | Repeat |
G [auth 3] | PF03178 | CPSF A subunit region (CPSF_A) | CPSF A subunit region | - | Repeat |
H [auth 4] | 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 |
I [auth 5] | PF07189 | Splicing factor 3B subunit 10 (SF3b10) (SF3b10) | Splicing factor 3B subunit 10 (SF3b10) | - | Family |