6I9R

Large subunit of the human mitochondrial ribosome in complex with Virginiamycin M and Quinupristin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrial 0188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
Find proteins for Q9BYC8 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrial 165Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrial 292Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrial 3188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrial 4103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrial 5423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrial 6380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrial 7338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrial 8206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrial 9137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrial D305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrial E348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrial F311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrial H267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrial I261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrial J192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrial K178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrial L145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
Find proteins for Q6P1L8 (Homo sapiens)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrial M296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
Find proteins for Q9P015 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrial N251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
Find proteins for Q9NX20 (Homo sapiens)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrial O175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18, isoform CRA_b P179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
Find proteins for A8K9D2 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrial Q292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrial R149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
Find proteins for Q9BYC9 (Homo sapiens)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrial S205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
Find proteins for Q7Z2W9 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrial T212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrial U153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
Find proteins for Q16540 (Homo sapiens)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrial V216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
Find proteins for Q96A35 (Homo sapiens)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrial W148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
Find proteins for Q9P0M9 (Homo sapiens)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrial X256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
Find proteins for Q13084 (Homo sapiens)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrial Y250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
Find proteins for Q9HD33 (Homo sapiens)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrial Z161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
Find proteins for Q8TCC3 (Homo sapiens)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrial a142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
Find proteins for Q9Y6G3 (Homo sapiens)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrial b215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
Find proteins for Q8N983 (Homo sapiens)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrial c332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
Find proteins for Q9H9J2 (Homo sapiens)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrial d306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
Find proteins for Q9BRJ2 (Homo sapiens)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrial e279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrial f212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrial g166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
Find proteins for Q13405 (Homo sapiens)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrial h158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
Find proteins for Q8N5N7 (Homo sapiens)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrial i128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA j123Homo sapiensMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrial k112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
Find proteins for Q96EL3 (Homo sapiens)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrial l138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrial m128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrial o102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
Find proteins for Q9BQC6 (Homo sapiens)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrial p206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
Find proteins for Q14197 (Homo sapiens)
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1 q222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
Find proteins for Q8TAE8 (Homo sapiens)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrial r196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
Find proteins for Q9NVS2 (Homo sapiens)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrial s439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
Find proteins for Q9NP92 (Homo sapiens)
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Entity ID: 11
MoleculeChainsLengthOrganismImage
16S rRNAA1557Homo sapiens
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Entity ID: 12
MoleculeChainsLengthOrganismImage
tRNA ValB69Homo sapiens
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H8Q
Query on H8Q

Download Ideal Coordinates CCD File 
A
~{N}-[(3~{S},6~{R},12~{R},15~{S},16~{S},19~{S},22~{S},25~{S})-25-[[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]sulfanylmethyl]-3-[[4-(dimethylamino)phenyl]methyl]-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptakis(oxidanylidene)-19-phenyl-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide
C53 H67 N9 O10 S
WTHRRGMBUAHGNI-QGNGWGIWSA-N
 Ligand Interaction
H8T
Query on H8T

Download Ideal Coordinates CCD File 
A
(10~{R},11~{R},12~{E},17~{E},19~{E},21~{S})-11,19-dimethyl-21-oxidanyl-10-propan-2-yl-9,26-dioxa-3,15,28-triazatricyclo[23.2.1.0^{3,7}]octacosa-1(27),4,6,12,17,19,25(28)-heptaene-2,8,14,23-tetrone
C28 H33 N3 O7
CNTGCXRBDCXZRN-FQTGFAPKSA-N
 Ligand Interaction
G
Query on G

Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
0, 4, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
9, A, D, L, M, g, o
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Structure summary
  • Version 1.2: 2020-07-22
    Changes: Database references