4V84

Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.

Zhu, J.Korostelev, A.Costantino, D.A.Donohue, J.P.Noller, H.F.Kieft, J.S.

(2011) Proc.Natl.Acad.Sci.USA 108: 1839-1844

  • DOI: 10.1073/pnas.1018582108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a l ...

    Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a lack of high-resolution structures of IRES RNAs bound to their cellular targets. Prompted by the universal phylogenetic conservation of the ribosomal P site, we solved the crystal structures of proposed P site binding domains from two intergenic region IRES RNAs bound to bacterial 70S ribosomes. The structures show that these IRES domains nearly perfectly mimic a tRNA • mRNA interaction. However, there are clear differences in the global shape and position of this IRES domain in the intersubunit space compared to those of tRNA, supporting a mechanism for IRES action that invokes hybrid state mimicry to drive a noncanonical mode of translocation. These structures suggest how relatively small structured RNAs can manipulate complex biological machines.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB
234Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD
208Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE
151Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsE (rps5)
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, CF
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsF (rps6)
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG
155Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, CH
138Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsH (rps8)
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI
127Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ
98Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsJ (rps10)
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK
119Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL
124Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsL (rps12)
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM
116Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
AN, CN
60Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsZ (rps14, rpsN)
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsO (rps15)
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP
83Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ
99Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsQ (rps17)
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62658
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR
70Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS
78Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsS (rps19)
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT
99Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62661
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
AU, CU
24Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62613
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BC, DC
271Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplB
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD, DD
204Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I04
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE, DE
202Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I05
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF, DF
181Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I16
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG, DG
159Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I19
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BH, DH
145Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GV5
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
BI, DI
65Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplJ
Find proteins for Q72GS1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GS1
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BJ, DJ
137Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BK, DK
122Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q72I14 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I14
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BL, DL
146Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I23
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BM, DM
136Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q72I11 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I11
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BN, DN
117Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BO, DO
98Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I20
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BP, DP
137Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JU9
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BQ, DQ
116Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BR, DR
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS, DS
112Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I09
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT, DT
92Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I06
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU, DU
100Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I15
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV, DV
188Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BW, DW
76Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q72HR3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR3
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BX, DX
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72G84
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BY, DY
62Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BZ, DZ
59Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I22
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B1, D1
30Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B2, D2
52Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62652
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B3, D3
44Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmG
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B4, D4
48Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B5, D5
63Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L77
Entity ID: 1
MoleculeChainsLengthOrganism
ribosomal RNA 16SAA,CA1506Thermus thermophilus HB27
Entity ID: 22
MoleculeChainsLengthOrganism
RNA (34-MER)AV,CV43Thermus thermophilus HB27
Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNABA,DA2879Thermus thermophilus HB27
Entity ID: 24
MoleculeChainsLengthOrganism
5S ribosomal RNABB,DB119Thermus thermophilus HB27
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
AD, AN, CD, CN
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, AD, AV, B2, BA, BB, BK, CA, CP, CV, D2, D4, DA, DB, DE, DG
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 210.690α = 90.00
b = 451.660β = 90.00
c = 614.250γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2018-04-11
    Type: Data collection, Database references, Source and taxonomy, Structure summary