6HMA

Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit

Eyal, Z.Cimicata, G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
274Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P60430
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
215Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW06
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
206Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW07
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
158Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW18
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
175Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW21
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
H
145Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW38
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
I
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW16
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
J
146Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplO
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0F8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
K
137Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW13
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
L
120Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW33
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
M
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW22
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
N
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ42
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
O
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
P
102Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXS8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
Q
112Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW11
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
R
89Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW08
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
S
103Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW17
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
T
94Staphylococcus aureus (strain USA300)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q2FJE0 (Staphylococcus aureus (strain USA300))
Go to UniProtKB:  Q2FJE0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
U
79Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXT0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
V
49Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ60
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
W
67Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW14
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
X
58Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0G2
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Z
48Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmF
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZF1
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
47Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmG1
Find proteins for Q2FYU6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FYU6
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
43Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FUQ0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ0
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
37Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW29
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAA2923Staphylococcus aureus
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB115Staphylococcus aureus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, J, K, U, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
5MU
Query on 5MU
A
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
A
RNA LINKINGC11 H16 N5 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release