OCA Atlas for 5H1S

5H1S

Ribosome

date

Oct 11, 2016

title

Structure Of The Large Subunit Of The Chloro-Ribosome

authors

T.Ahmed, Z.Yin, S.Bhushan

compound

source

Molecule: 23s Rrna
Chain: A

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: Spinach Chloroplast 4.5s Rrna
Chain: C
Synonym: 4.8s Rrna

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 5s Rrna
Chain: B

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L13, Chloroplastic
Chain: L
Synonym: Cl13

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L14, Chloroplastic
Chain: M
Synonym: Ribosomal Protein Cs-L29

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L15
Chain: N
Fragment: Unp Residues 80-271
Synonym: L15

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L16, Chloroplastic
Chain: O
Synonym: Ribosomal Protein Cs-L24

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L17
Chain: P
Fragment: Unp Residues 11-126
Synonym: L17

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L18
Chain: Q
Fragment: Unp Residues 44-166
Synonym: L18

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L19, Chloroplastic
Chain: R
Synonym: Cl19

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L20, Chloroplastic
Chain: S

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L21, Chloroplastic
Chain: T
Synonym: Cl21,Cs-L7

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L22, Chloroplastic
Chain: U
Synonym: Ribosomal Protein Cs-L13

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L23, Chloroplastic
Chain: V
Synonym: Prpl23

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L24, Chloroplastic
Chain: W
Synonym: Cl24

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L27
Chain: X
Fragment: Unp Residues 58-194

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L28
Chain: Y
Fragment: Unp Residues 72-148
Synonym: L28

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L29
Chain: Z
Fragment: Unp Residues 60-168
Synonym: L29

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L2, Chloroplastic
Chain: E
Synonym: Ribosomal Protein Cs-L4

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L32, Chloroplastic
Chain: b

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L33, Chloroplastic
Chain: c

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L34, Chloroplastic
Chain: d
Synonym: Cl34

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L35, Chloroplastic
Chain: e
Synonym: Cl35

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L36, Chloroplastic
Chain: f

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L3
Chain: F
Fragment: Unp Residues 85-305
Synonym: L3

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L4, Chloroplastic
Chain: G
Synonym: R-Protein L4

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L5, Chloroplastic
Chain: H

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L6
Chain: I
Fragment: Unp Residues 39-220
Synonym: L6

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L9
Chain: J
Fragment: Unp Residues 42-196

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein 5 Alpha, Chloroplastic
Chain: g
Synonym: 50s Ribosomal Protein L40,Cl40,Plastid-Specific 50 Ribosomal Protein 5 Alpha,Psrp-5;

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein L31
Chain: a
Fragment: Unp Residues 37-130

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: 50s Ribosomal Protein 6, Chloroplastic
Chain: h
Synonym: Cl25,Plastid-Specific 50s Ribosomal Protein 6,Psrp

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

symmetry

Space Group: P 1

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
1.000	1.000	1.000	90.00	90.00	90.00

method

Electron Microscopy

resolution

3.50 Å

Gene
Ontology

Chain	Function	Process	Component
E
F
G
H
I
J
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
a
b
c
d
e
f
g
h

Primary reference

Cryo-EM structure of the large subunit of the spinach chloroplast ribosome., Ahmed T, Yin Z, Bhushan S, Sci Rep. 2016 Oct 20;6:35793. doi: 10.1038/srep35793. PMID:27762343

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1560 Kb) [Save to disk]

Biological Unit Coordinates (5h1s.pdb1.gz) 1548 Kb

CSU: Contacts of Structural Units for 5H1S

Retrieve 5H1S in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5H1S from S2C, [Save to disk]

View 5H1S in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5H1S

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5h1s] [5h1s_b] [5h1s_N] [5h1s_c] [5h1s_B] [5h1s_H] [5h1s_Z] [5h1s_g] [5h1s_R] [5h1s_a] [5h1s_I] [5h1s_P] [5h1s_F] [5h1s_S] [5h1s_f] [5h1s_L] [5h1s_G] [5h1s_A] [5h1s_X] [5h1s_Q] [5h1s_Y] [5h1s_V] [5h1s_h] [5h1s_O] [5h1s_C] [5h1s_U] [5h1s_d] [5h1s_J] [5h1s_W] [5h1s_E] [5h1s_T] [5h1s_e] [5h1s_M]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 5H1S

Community annotation for 5H1S at PDBWiki (http://pdbwiki.org)

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