NPIDB: 6EML structure

General information

PDB ID

6EML

Title

CRYO-EM STRUCTURE OF A LATE PRE-40S RIBOSOMAL SUBUNIT FROM SACCHAROMYCES CEREVISIAE

PDB header

RIBOSOME

Date

2017-10-02

Experimental method

ELECTRON MICROSCOPY

Resolution (A)

3.6

Kind

rna

Organism

SACCHAROMYCES CEREVISIAE S288C


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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:

pdb6eml.pdb	DBCEFHIKLNPQRSTUVWXYZabcdftgpre		2	0

Biounits:

6eml.pdb1.pdb	DBCEFHIKLNPQRSTUVWXYZabcdftgpre		2	1

Pfam domains
Name:	Type:	Domain:	E-value:	Significance:	Clan:	Prot. chain:	Start res.:	End res.:	Nuc. chains:	Int. mode:	Action:

Ribosomal_S7	Domain	P26783_76-225	4.5e-32	1	No_clan	B	72	225	2
Ribosomal_S8	Domain	P0C0W1_5-130	5e-24	1	No_clan	b	5	130	2
Ribosomal_L7Ae	Domain	P48589_26-123	1.2e-22	1	CL0101	D	26	123	2
Ribosomal_S19	Domain	Q01855_43-128	1.6e-32	1	No_clan	E	43	128	2
Ribosomal_S27	Domain	P05759_102-147	1.8e-25	1	CL0167	N	102	147	2
Rio2_N	Domain	P40160_8-91	2.4e-29	1	CL0123	r	8	91	2
Ribosomal_S5	Domain	P25443_76-140	1.1e-26	1	CL0196	R	76	140	2
Ribosomal_S5_C	Domain	P25443_159-230	4.9e-24	1	CL0329	R	159	230	2
RS4NT	Domain	P0CX35_3-39	1.5e-19	1	No_clan	S	3	39	2
S4	Domain	P0CX35_42-90	1.6e-08	1	CL0492	S	42	90	2
AARP2CN	Domain	Q07381_234-309	1.5e-21	1	No_clan	t	234	336	2
S4	Domain	O13516_107-153	3.3e-12	1	CL0492	W	107	153	2
Ribosomal_S17	Domain	P0CX47_73-141	8.4e-28	1	CL0021	X	73	141	2
Ribosomal_S13_N	Domain	P05756_2-60	8.1e-28	1	No_clan	Y	2	60	2
Ribosomal_S15	Domain	P05756_70-149	3.2e-15	1	CL0600	Y	70	149	2
Ribosomal_S21e	Family	P0C0V8_1-80	5.8e-40	1	No_clan	a	1	80	2
Ribosom_S12_S23	Family	P0CX29_31-144	2.1e-51	1	CL0021	c	31	144	2
Ribosomal_S17e	Family	P02407_2-126	6.3e-46	1	No_clan	C	2	122	2
Ribosomal_S24e	Family	P0CX31_24-102	6.5e-35	1	No_clan	d	24	102	2
Bystin	Family	P38333_205-465	2.1e-116	1	No_clan	e	205	465	2
Ribosomal_S9	Family	P0CX51_11-143	1.3e-32	1	CL0329	F	11	143	2
Ribosomal_S27e	Family	P35997_28-82	5e-30	1	CL0167	f	28	82	2
Ribosomal_S30	Family	P0CX33_3-61	8.2e-29	1	No_clan	g	3	61	2
Ribosomal_S13	Family	P0CX55_16-131	1.3e-47	1	CL0303	H	16	131	2
Ribosomal_S19e	Family	P07280_5-142	8.8e-54	1	CL0123	I	5	142	2
Ribosomal_S25	Family	Q3E792_42-104	1.3e-24	1	CL0123	K	42	104	2
Ribosomal_S28e	Family	P0C0X0_5-66	1.2e-32	1	CL0021	L	5	66	2
Ribosomal_S2	Family	P32905_110-183	2.9e-14	1	CL0067	P	111	183	2
Ribosomal_S2	Family	P32905_17-117	9.4e-10	1	CL0067	P	17	116	2
Ribosomal_S3Ae	Family	P33442_20-221	7.6e-88	1	No_clan	Q	20	221	2
RIO1	Family	P40160_108-288	3e-35	1	CL0016	r	108	287	2
Ribosomal_S4e	Family	P0CX35_95-169	2.1e-38	1	No_clan	S	95	169	2
40S_S4_C	Family	P0CX35_212-259	3.8e-26	1	No_clan	S	212	259	2
KOW	Family	P0CX35_177-211	3.8e-06	1	CL0107	S	177	211	2
RIBIOP_C	Family	Q07381_486-779	1.2e-106	1	CL0575	t	486	779	2
Ribosomal_S6e	Family	P0CX37_1-126	6e-58	1	No_clan	T	1	126	2
Ribosomal_S7e	Family	P26786_5-187	6.2e-80	1	CL0652	U	5	187	2
Ribosomal_S8e	Family	P0CX39_2-184	1.8e-59	1	No_clan	V	2	184	2
Ribosomal_S17_N	Family	P0CX47_8-71	8.4e-32	1	No_clan	X	8	71	2
Ribosomal_S11	Family	P06367_15-129	3.2e-46	1	CL0267	Z	15	133	2

SCOP domains
No SCOP domains

GO terms
Protein chains:	GO type:	GO description:
a=1-87	P	endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
c=1-145	C	ribosome
c=1-145	P	maintenance of translational fidelity
c=1-145	P	regulation of translational fidelity
d=1-135	C	cytosolic small ribosomal subunit
d=1-135	C	mitochondrion
d=1-135	F	structural constituent of ribosome
d=1-135	P	cytoplasmic translation
d=1-135	P	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
e=1-483	C	preribosome, small subunit precursor
e=1-483	F	snoRNA binding
e=1-483	P	poly(A)+ mRNA export from nucleus
e=1-483	P	rRNA processing
f=1-82	F	metal ion binding
f=1-82	P	ribosomal small subunit assembly
g=1-63	C	cytoplasmic stress granule
L=1-67	P	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
N=1-152	F	protein tag
N=1-152	F	ubiquitin protein ligase binding
N=1-152	P	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S)
N=1-152	P	modification-dependent protein catabolic process
N=1-152	P	protein ubiquitination
N=1-152	P	ribosome biogenesis
p=1-274	C	90S preribosome
p=1-274	C	cytoplasm
p=1-274	C	nucleolus
p=1-274	C	nucleus
p=1-274	F	RNA binding
p=1-274	F	unfolded protein binding
p=1-274	P	endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
p=1-274	P	endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
p=1-274	P	proteasome assembly
R=1-254	C	nucleoplasm
R=1-254	C	small-subunit processome
R=1-254	F	small ribosomal subunit rRNA binding
R=1-254	P	positive regulation of translational fidelity
R=1-254	P	rRNA export from nucleus
R=1-254	P	rRNA methylation
R=1-254	P	translation
r=1-425	C	cytosol
r=1-425	F	ATP binding
r=1-425	F	protein kinase activity
r=1-425	F	protein serine/threonine kinase activity
r=1-425	P	maturation of SSU-rRNA
r=1-425	P	positive regulation of RNA import into nucleus
t=1-788	F	GTP binding
t=1-788	F	GTPase activity
t=1-788	F	ribonucleoprotein complex binding
t=1-788	F	U3 snoRNA binding
t=1-788	P	endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
U=1-190	P	ribosomal small subunit biogenesis
W=1-197	C	small ribosomal subunit
W=1-197	F	rRNA binding
Z=1-137	F	mRNA 5'-UTR binding
Z=1-137	F	mRNA binding

Sequences

Download file with secondary structure created by Stride

6eml.pdb1.pdb: [ download sequences in FASTA format ]

a (protein):