General information
PDB ID 4D5L
Title CRYO-EM STRUCTURES OF RIBOSOMAL 80S COMPLEXES WITH TERMINATION FACTORS AND CRICKET PARALYSIS VIRUS IRES REVEAL THE IRES IN THE TRANSLOCATED STATE
PDB header RIBOSOME
Date 2014-11-05
Experimental method ELECTRON MICROSCOPY
Resolution (A) 9
Kind rna
Organism ORYCTOLAGUS CUNICULUS
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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:
pdb4d5l.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefg 1 0
Biounits:
4d5l.pdb1.pdb ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefg 1 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Ribosomal_S5 Domain G1TUT9_82-146 1.2e-32 1 CL0196 C 102 166 1   
Ribosomal_S5_C Domain G1TUT9_165-236 2.1e-28 1 CL0329 C 185 256 1   
Ribosomal_S3_C Domain G1TNM3_143-226 5.6e-23 1 No_clan D 105 188 1   
KH_2 Domain G1TNM3_58-134 0.000000000019 1 CL0007 D 20 96 1   
RS4NT Domain G1TK17_3-39 7.1e-22 1 No_clan E 3 39 1   
S4 Domain 0.00016 0 CL0492 E 42 90 1
Ribosomal_S7 Domain G1TFM5_51-204 2.7e-37 1 No_clan F 51 204 1   
Ribosomal_S27 Domain G1SK22_102-147 6.8e-29 1 CL0167 f 102 147 1   
S4 Domain B7NZS8_108-154 0.000000000038 1 CL0492 J 108 154 1   
S10_plectin Domain G1T168_63-155 3.1e-50 1 No_clan K 3 95 1   
Ribosomal_S17 Domain G1TRM4_75-144 1.5e-29 1 CL0021 L 75 144 1   
Ribosomal_L7Ae Domain G1SFR8_16-111 2.2e-30 1 CL0101 M 16 111 1   
Ribosomal_S13_N Domain G1SP51_2-60 2.3e-31 1 No_clan N 2 60 1   
Ribosomal_S15 Domain G1SP51_70-148 9.2e-16 1 CL0600 N 70 149 1   
Ribosomal_S19 Domain G1U0Q2_43-128 8.4e-41 1 No_clan P 43 128 1   
Ribosomal_S8 Domain G1TG89_5-130 2.1e-22 1 No_clan W 5 130 1   
Ribosomal_S26e Family G1TFE8_2-97 8.5e-51 1 No_clan a 2 97 1   
Ribosomal_S2 Family G1TWL4_111-184 0.00000000000071 1 CL0067 A 111 184 1   
Ribosomal_S2 Family G1TWL4_18-118 0.000000000037 1 CL0067 A 18 118 1   
40S_SA_C Family G1TWL4_202-219 0.000032 1 No_clan A 202 219   
Ribosomal_S3Ae Family G1SS70_21-221 1.7e-106 1 No_clan B 21 221 1   
Ribosomal_S27e Family G1TZ76_28-82 1.2e-30 1 CL0167 b 28 82 1   
Ribosomal_S28e Family G1TIB4_8-68 4.3e-35 1 CL0021 c 8 68 1   
Ribosomal_S14 Family G1U7M4_6-55 0.0000000000000022 1 No_clan d 6 55 1   
Ribosomal_S4e Family G1TK17_95-169 1.2e-37 1 No_clan E 95 169 1   
40S_S4_C Family G1TK17_212-258 1.1e-28 1 No_clan E 212 258 1   
Ribosomal_S30 Family G1T8A2_80-130 1.6e-26 1 No_clan e 6 56 1   
KOW Family G1TK17_177-211 0.000019 1 CL0107 E 177 211 1   
Ribosomal_S6e Family G1TM55_1-126 7.6e-70 1 No_clan G 1 126 1   
Ribosomal_S7e Family G1SVB0_7-191 6.8e-94 1 CL0652 H 7 191 1   
Ribosomal_S8e Family G1TJW1_2-190 3.1e-62 1 No_clan I 2 190 1   
Ribosomal_S4 Family B7NZS8_9-140 0.0000094 1 CL0492 J 9 107 1   
Ribosomal_S17_N Family G1TRM4_5-73 3.3e-37 1 No_clan L 5 73 1   
Ribosomal_S11 Family G1U472_29-147 2.7e-47 1 CL0267 O 29 147 1   
Ribosomal_S9 Family G1SGX4_40-172 4.2e-34 1 CL0329 Q 14 146 1   
Ribosomal_S17e Family G1TU13_2-122 1.6e-54 1 No_clan R 2 119 1   
Ribosomal_S13 Family G1TPG3_14-142 2.7e-56 1 CL0303 S 14 142 1   
Ribosomal_S19e Family G1TN62_5-141 1.4e-58 1 CL0123 T 5 141 1   
Ribosomal_S10 Family G1SIZ2_21-115 3e-31 1 No_clan U 21 115 1   
Ribosomal_S21e Family G1TM82_1-80 3e-43 1 No_clan V 1 80   
Ribosom_S12_S23 Family G1SZ47_29-140 1e-51 1 CL0021 X 29 140 1   
Ribosomal_S24e Family G1TS40_24-102 5e-46 1 No_clan Y 24 102 1   
Ribosomal_S25 Family G1TDB3_40-112 2.3e-38 1 CL0123 Z 40 112 1   
WD40 Repeat G1SJB4_224-260 0.0000000068 1 CL0186 g 95 133 1   
WD40 Repeat G1SJB4_224-260 0.0000000091 1 CL0186 g 53 91 1   
WD40 Repeat G1SJB4_224-260 0.000036 1 CL0186 g 136 178 1   
WD40 Repeat G1SJB4_224-260 0.000047 1 CL0186 g 182 220 1   
WD40 Repeat G1SJB4_224-260 0.00011 1 CL0186 g 224 260   
SCOP domains
No SCOP domains
GO terms
No GO terms
Sequences
Download file with secondary structure created by Stride  
4d5l.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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D (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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M (protein): 
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N (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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1 (rna): 
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