General information
PDB ID 6EM5
Title STATE D ARCHITECTURAL MODEL (NSA1-TAP FLAG-YTM1) - VISUALIZING THE ASSEMBLY PATHWAY OF NUCLEOLAR PRE-60S RIBOSOMES
PDB header RIBOSOME
Date 2017-10-01
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.3
Kind rna
Organism
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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:
pdb6em5.pdb LMNQRSTUZcdefgijkEGOVXYhBCHAKmDWlbonrstyzpquvwIJx345FP 261 0
Biounits:
6em5.pdb1.pdb LMNQRSTUZcdefgijkEGOVXYhBCHAKmDWlbonrstyzpquvwIJx345FP 261 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Brix Domain Q08235_38-224 3e-38 1 CL0458 A 38 224   
NOGCT Domain Q02892_396-449 3.2e-27 1 No_clan b 396 449 1   
FeoB_N Domain 0.0000097 1 CL0023 b 168 246
Ribos_L4_asso_C Domain P10664_272-348 9.3e-30 1 No_clan C 272 348 1   
Ribosomal_L7Ae Domain P14120_9-102 4.7e-23 1 CL0101 c 9 102 12   
DUF4217 Domain Q03532_425-484 3.6e-17 1 No_clan D 425 481   
Ribosomal_L35Ae Domain P05744_7-101 3.5e-42 1 CL0575 f 7 101 1   
Ribosomal_L30_N Domain P05737_8-79 1.6e-20 1 No_clan F 8 79 1   
Ribosomal_L30 Domain P05737_84-134 1.2e-19 1 No_clan F 84 134 1   
Ribosomal_L7Ae Domain P17076_117-212 1.7e-23 1 CL0101 G 112 212 1   
Ribosomal_L6 Domain P05738_12-85 1.5e-16 1 No_clan H 12 85 1   
Ribosomal_L6 Domain P05738_97-178 0.000000000000049 1 No_clan H 97 178   
UvrD-helicase Domain 0.00068 0 CL0023 I 230 550 1
Ribosomal_L1 Domain P38779_42-287 1.7e-34 1 No_clan K 44 287 16   
BOP1NT Domain Q04660_165-426 8.5e-104 1 No_clan m 165 426 1   
RRM_1 Domain P53927_93-163 5e-18 1 CL0221 o 93 163 1   
Ribosomal_L22 Domain P05740_17-151 6.2e-25 1 No_clan P 17 151 12   
Methyltr_RsmF_N Domain P40991_244-335 0.00000006 1 CL0063 q 244 335   
Ribosomal_L18A Domain P0CX23_4-127 1.8e-53 1 No_clan S 4 127 1   
Ribosomal_L30 Domain P40693_142-194 0.000000000013 1 No_clan t 142 194 6   
Ribosomal_L14 Domain P0CX41_17-137 2.2e-33 1 No_clan V 17 137 1   
Spb1_C Domain 5.8e-49 1 No_clan w 321 794
Spb1_C Domain 0.00000000000012 1 No_clan w 752 835 1
Brix Domain P38805_101-269 7.7e-21 1 CL0458 x 100 269 1   
Ribosomal_L28e Family P10962_5-118 1.2e-40 1 No_clan 3 5 118 1   
Mak16 Family P10962_138-170 0.000000000000093 1 No_clan 3 138 174   
Nop52 Family P35178_4-243 2.9e-66 1 No_clan 4 5 244 1   
Ribosomal_L3 Family P14126_12-366 4.5e-108 1 CL0575 B 12 266 1   
NOG1 Family Q02892_234-288 2.6e-23 1 CL0023 b 234 301 1   
Ribosomal_L4 Family P10664_20-261 7.5e-44 1 No_clan C 20 261 12   
Ribosomal_L31e Family P0C2H8_9-87 1.2e-40 1 No_clan d 6 87 1   
Helicase_C Family Q03532_275-379 2.3e-23 1 CL0023 D 275 389   
Ribosomal_L32e Family P38061_14-121 6.9e-47 1 No_clan e 14 121 1   
Ribosomal_L6e Family 0.000000000000001 1 No_clan E 107 176 1
Ribosomal_L6e Family 0.00000000000011 1 No_clan E 71 133 1
Ribosomal_L34e Family P87262_2-94 1e-41 1 No_clan g 2 94 1   
Ribosomal_L29 Family P0CX84_7-61 5.1e-16 1 CL0346 h 7 61 1   
Ribosomal_L36e Family O14455_27-99 3e-28 1 No_clan i 29 99 1   
CBF Family Q07896_472-647 0.000000000000023 1 No_clan I 472 633   
NOC3p Family Q07896_136-227 0.000000000000042 1 No_clan I 136 227   
Ebp2 Family P36049_196-327 2.4e-52 1 No_clan J 196 327   
Ribosomal_L37e Family P49166_14-54 5e-21 1 CL0167 j 14 54 1   
Ribosomal_L38e Family P49167_2-78 3e-27 1 No_clan k 2 78 1   
Ribosomal_L13e Family Q12690_8-129 1.2e-62 1 No_clan L 8 129 1   
UPF0113 Family Q08962_96-174 0.00000000000044 1 CL0178 l 1 174 1   
Ribosomal_L14e Family P36105_54-128 9.1e-33 1 CL0107 M 54 128 1   
KOW Family 0.00074 0 CL0107 M 17 47
Pescadillo_N Family P53261_5-267 1.6e-123 1 No_clan n 5 358 12   
Ribosomal_L15e Family 6.1e-47 1 CL0652 N 70 190 12
Ribosomal_L15e Family 4e-30 1 CL0652 N 2 88 12
BRCT_2 Family P53261_357-448 0.0000000000045 1 CL0459 n 357 448   
Ribosomal_L13 Family P26784_6-118 0.000000018 1 No_clan O 6 118 1   
Methyltr_RsmB-F Family P40991_338-547 4.5e-80 1 CL0063 q 338 547 1   
Ribosomal_L18 Family P0CX49_15-148 1e-67 1 CL0588 Q 15 148 1   
Ribosomal_S8e Family P40078_18-260 3.4e-33 1 No_clan r 30 260 1   
Ribosomal_L19e Family 2.7e-21 1 No_clan R 3 91 1
Ribosomal_L19e Family 7.7e-19 1 No_clan R 89 146 1
Ribosomal_L22e Family P05749_11-108 1.4e-36 1 No_clan U 11 108 1   
Ribosomal_L24e Family Q07915_2-66 1.8e-32 1 CL0175 u 1 66   
Nop16 Family 1.1e-23 1 No_clan v 66 223 1
Nop16 Family 8.8e-23 1 No_clan v 5 164 1
FtsJ Family P25582_25-202 5e-55 1 CL0063 w 25 202 1   
DUF3381 Family P25582_254-329 3e-24 1 No_clan w 219 752   
Ribosomal_L10 Family P33201_18-120 8e-20 1 No_clan W 18 120   
Ribosomal_L23eN Family P04456_3-53 2.6e-19 1 No_clan X 3 53 12   
Ribosomal_L23 Family P04456_61-135 4.5e-16 1 No_clan X 61 135 1   
eIF-6 Family Q12522_4-204 2.5e-82 1 CL0197 y 4 204 12   
Ribosomal_L26 Family P05743_9-122 4.7e-36 1 No_clan Y 9 122 12   
KOW Family P05743_52-90 0.000034 1 CL0107 Y 52 90 12   
Ribosomal_L27e Family P0C2H6_52-136 1.4e-36 1 No_clan Z 52 136   
DUF2423 Family P38202_2-44 1.5e-18 1 No_clan z 2 44 1   
WD40 Repeat Q04660_427-465 0.000000002 1 CL0186 m 427 465   
WD40 Repeat Q04660_427-465 0.00015 1 CL0186 m 764 806   
WD40 Repeat Q12024_134-171 0.00000007 1 CL0186 p 358 404   
WD40 Repeat Q12024_95-131 0.000029 1 CL0186 p 134 171   
WD40 Repeat Q12024_134-171 0.00061 1 CL0186 p 198 235   
SCOP domains
No SCOP domains
GO terms
No GO terms
Sequences
Download file with secondary structure created by Stride  
6em5.pdb1.pdb:   [ download sequences in FASTA format ]
3 (protein): 
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4 (protein): 
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5 (protein): 
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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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2 (rna): 
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6 (rna): 
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