General information
PDB ID 5GMK
Title CRYO-EM STRUCTURE OF THE CATALYTIC STEP I SPLICEOSOME (C COMPLEX) AT 3.4 ANGSTROM RESOLUTION
PDB header RNA BINDING PROTEIN/RNA
Date 2016-07-14
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.4
Kind rna
Organism SACCHAROMYCES CEREVISIAE S288C
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
PRIDB
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb5gmk.pdb ACJOPQRSTZcdFGHIvnopqrtkihjlmgsuwxyzeab DELMBN 0
Biounits:
5gmk.pdb1.pdb ACJOPQRSTZcdFGHIvnopqrtkihjlmgsuwxyzeab DELMBN 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
PROCN Domain P33334_470-874 1.7e-218 1 No_clan A 470 874 BDELN   
PRP8_domainIV Domain P33334_1840-2061 9.5e-118 1 No_clan A 1824 2061 M   
PRO8NT Domain P33334_131-282 2.3e-79 1 No_clan A 131 282 DE   
U5_2-snRNA_bdg Domain P33334_1282-1415 3.2e-69 1 No_clan A 1282 1415 BM   
RRM_4 Domain P33334_1059-1150 2.5e-47 1 No_clan A 1059 1150 L   
U6-snRNA_bdg Domain P33334_1514-1672 2.7e-41 1 CL0363 A 1577 1672 BL   
RRM_5 Domain P40567_29-110 8.2e-09 1 CL0221 a 29 110 L   
GTP_EFTU Domain P36048_131-442 2.9e-36 1 CL0023 C 131 443 DE   
GTP_EFTU_D2 Domain 3.3e-16 1 CL0575 C 481 578
EFG_C Domain P36048_856-948 1.2e-14 1 CL0437 C 856 948   
EFG_IV Domain P36048_738-854 6.4e-13 1 CL0329 C 738 854   
Myb_DNA-binding Domain Q03654_10-56 3.2e-12 1 CL0123 c 10 56 LE   
Myb_DNA-binding Domain Q03654_63-106 3.8e-07 1 CL0123 c 63 106 D   
LSM Domain Q06217_44-106 2.5e-17 1 CL0527 e 44 106 L   
LSM Domain Q06217_37-106 1e-17 1 CL0527 g 37 106 D   
Cir_N Domain P53854_11-42 3.6e-11 1 No_clan G 11 42 DL   
LSM Domain P54999_17-83 2.1e-18 1 CL0527 h 17 83 DEMN   
LSM Domain Q12330_19-92 2e-16 1 CL0527 i 19 92 D   
SYF2 Domain P53277_92-211 2.1e-07 1 No_clan I 93 210 LE   
LSM Domain P40204_5-73 3.6e-16 1 CL0527 j 5 73 BD   
LSM Domain P40018_10-97 2.1e-22 1 CL0527 k 10 97 D   
LSM Domain P43321_9-74 2.1e-16 1 CL0527 l 9 74 D   
LSM Domain Q02260_5-97 6.1e-27 1 CL0527 m 5 97 D   
Prp19 Domain P32523_77-139 5.9e-26 1 No_clan o 62 139   
U-box Domain 0.0001 1 CL0229 o 1 84
Prp19 Domain P32523_77-139 6.2e-26 1 No_clan p 62 139 DE   
U-box Domain 0.00011 1 CL0229 p 1 84
Prp19 Domain P32523_77-139 2.2e-25 1 No_clan q 59 139   
Torus Domain Q12046_4-114 5e-33 1 CL0537 R 4 114 EN   
Prp19 Domain P32523_77-139 5.8e-26 1 No_clan r 62 139 EN   
RRM_1 Domain Q12046_149-206 3.7e-06 1 CL0221 R 149 206 EN   
U-box Domain 0.00012 1 CL0229 r 1 85 EN
LSM Domain P40018_10-97 1.9e-22 1 CL0527 s 10 97 DEL   
G10 Domain P25337_1-155 6.1e-64 1 No_clan T 1 155 DE   
LSM Domain Q12330_19-92 2e-16 1 CL0527 u 19 92 L   
LSM Domain P54999_17-83 2.1e-18 1 CL0527 w 17 83 L   
LSM Domain P40204_5-73 3.6e-16 1 CL0527 x 5 73 L   
LSM Domain P43321_9-74 2.1e-16 1 CL0527 y 9 74 L   
LSM Domain Q02260_5-97 6.1e-27 1 CL0527 z 5 97 L   
HAT Family Q12309_180-211 1.2e-06 1 CL0020 d 180 211   
DUF572 Family P28320_9-116 3.7e-42 1 No_clan F 2 116 BELM   
Isy1 Family P21374_2-96 5.7e-33 1 No_clan H 2 96 DELMN   
SKIP_SNW Family P28004_90-247 6.2e-38 1 No_clan P 88 247 DLE   
Cwf_Cwc_15 Family 2.4e-05 0 No_clan S 4 133 DEL
Cwf_Cwc_15 Family 0.0001 0 No_clan S 126 175
BCAS2 Family 0.00026 0 No_clan t 1 175 DE
MA3 Family P53333_291-398 5.8e-26 1 CL0020 Z 291 398   
LRR_9 Repeat Q08963_33-162 6.5e-07 0 CL0022 b 51 162   
WD40 Repeat P40968_286-321 1.1e-06 1 CL0186 n 275 321   
WD40 Repeat P40968_197-234 1.9e-06 1 CL0186 n 192 234   
WD40 Repeat P40968_197-234 7e-05 1 CL0186 n 152 191   
WD40 Repeat Q12417_172-210 1.5e-05 1 CL0186 O 214 252 E   
WD40 Repeat Q12417_172-210 3.1e-05 1 CL0186 O 129 168   
WD40 Repeat Q12417_172-210 0.00026 1 CL0186 O 172 210   
WD40 Repeat Q12417_172-210 0.00058 1 CL0186 O 256 294   
SCOP domains
No SCOP domains
GO terms
No GO terms
Sequences
Download file with secondary structure created by Stride  
5gmk.pdb1.pdb:   [ download sequences in FASTA format ]
a (protein): 
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b (protein): 
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c (protein): 
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e (protein): 
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F (protein): 
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g (protein): 
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H (protein): 
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I (protein): 
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J (protein): 
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k (protein): 
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l (protein): 
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O (protein): 
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p (protein): 
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Q (protein): 
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R (protein): 
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s (protein): 
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T (protein): 
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u (protein): 
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v (protein): 
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w (protein): 
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x (protein): 
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y (protein): 
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Z (protein): 
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D (rna): 
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M (rna): 
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N (rna): 
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