ISDA: 4V4J

Deposition Date 2007-07-18

Release Date 2014-07-09

Last Version Date 2024-10-09

Entry Detail

PDB ID:

4V4J

Keywords:

RIBOSOME

Title:

Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 262724)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.83 Å

R-Value Free:

0.35

R-Value Work:

0.32

R-Value Observed:

0.32

Space Group:

I 4 2 2

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:GA (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:HA (auth: 3)
Chain Length:18
Number of Molecules:1
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Chain IDs:C (auth: A)
Chain Length:65
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP7 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:D (auth: B)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:E (auth: C)
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN8 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:F (auth: D)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN9 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:G (auth: E)
Chain Length:182
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:H (auth: F)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY8 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:I (auth: G)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:J (auth: H)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60488 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:K (auth: I)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP8 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:L (auth: J)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:M (auth: K)
Chain Length:141
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60489 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:N (auth: L)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:O (auth: M)
Chain Length:132
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:P (auth: N)
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60490 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:Q (auth: O)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60491 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:R (auth: P)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60492 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:S (auth: Q)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP3 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:T (auth: R)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:U (auth: S)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:V (auth: T)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:W (auth: U)
Chain Length:85
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60493 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein L28P
Chain IDs:X (auth: V)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60494 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:Y (auth: W)
Chain Length:2889
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein L30P
Chain IDs:Z (auth: X)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:AA (auth: Y)
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80339 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BA (auth: Z)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80340 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:CA (auth: a)
Chain Length:65
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SKU1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:DA (auth: b)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHR2 Pfam ID:PF00444

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:IA (auth: c)
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80371 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:JA (auth: d)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:KA (auth: e)
Chain Length:182
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:LA (auth: f)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:MA (auth: g)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:NA (auth: h)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:OA (auth: i)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY9 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:PA (auth: j)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80374 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:QA (auth: k)
Chain Length:141
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN7 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:RA (auth: l)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80376 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:SA (auth: m)
Chain Length:132
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:TA (auth: n)
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80377 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:UA (auth: o)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY6 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:VA (auth: p)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:WA (auth: q)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJH3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:XA (auth: r)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY7 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:YA (auth: s)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:ZA (auth: t)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:AB (auth: u)
Chain Length:85
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80380 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Chain IDs:BB (auth: v)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:23S LARGE SUBUNIT RIBOSOMAL RNA
Chain IDs:A (auth: w)
Chain Length:2889
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S LARGE SUBUNIT RIBOSOMAL RNA
Chain IDs:B (auth: x)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:16S RNA
Chain IDs:EA (auth: y)
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:P-site tRNAfMET
Chain IDs:FA (auth: z)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
2MG	EA	G	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
5MC	EA	C	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
7MG	EA	G	?
M2G	EA	G	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
MA6	EA	A	6N-DIMETHYLADENOSINE-5'-MONOPHOSHATE
PSU	EA	U	PSEUDOURIDINE-5'-MONOPHOSPHATE

Ligand Molecules

Primary Citation

Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.

Korostelev, A, Trakhanov, S, Asahara, H, Laurberg, M, Lancaster, L, Noller, H.F.Show

Proc.Natl.Acad.Sci.Usa 104 16840 16843 (2007)

PMID: 17940016 DOI: 10.1073/pnas.0707850104

Abstact

The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were biased along its helical axis, suggesting that during the first step of translocation, the SD helix moves along its helical screw axis. Contacts between the SD helix and the ribosome were primarily through interactions with helices 23a, 26, and 28 of 16S rRNA. Contact with the neck (helix 28) of the 30S subunit near its hinge point suggests that formation of the SD helix could affect positioning of the head of the 30S subunit for optimal interaction with initiator tRNA. The bulged U723 in helix 23a interacts with the minor groove of the SD helix at the C1539.G-10 base pair, explaining its selective conservation in bacteria and archaea.

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Protein

Chemical

Disease

Primary Citation of related structures