ISDA

Deposition Date 2010-09-02

Release Date 2014-07-09

Last Version Date 2024-10-23

Entry Detail

PDB ID:

4V5L

Keywords:

RIBOSOME

Title:

The structure of EF-Tu and aminoacyl-tRNA bound to the 70S ribosome with a GTP analog

Biological Source:

Source Organism:

ESCHERICHIA COLI (Taxon ID: 83333)
THERMUS THERMOPHILUS (Taxon ID: 300852)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.10 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S RRNA
Chain IDs:A (auth: AA)
Chain Length:1522
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB)
Chain Length:256
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC)
Chain Length:239
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD)
Chain Length:209
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Chain IDs:E (auth: AE)
Chain Length:162
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Chain IDs:F (auth: AF)
Chain Length:101
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Chain IDs:G (auth: AG)
Chain Length:156
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AH)
Chain Length:138
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI)
Chain Length:128
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P62669 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Chain IDs:J (auth: AJ)
Chain Length:105
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK)
Chain Length:129
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Chain IDs:L (auth: AL)
Chain Length:135
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM)
Chain Length:126
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80377 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14
Chain IDs:N (auth: AN)
Chain Length:61
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY6 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Chain IDs:O (auth: AO)
Chain Length:89
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Chain IDs:P (auth: AP)
Chain Length:88
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AQ)
Chain Length:105
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Chain IDs:R (auth: AR)
Chain Length:88
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Chain IDs:S (auth: AS)
Chain Length:93
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT)
Chain Length:106
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN THX
Chain IDs:U (auth: AU)
Chain Length:27
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:E-SITE TRNA PHE OR P-SITE TRNA PHE
Chain IDs:V (auth: AV), W (auth: AW)
Chain Length:76
Number of Molecules:2
Biological Source:ESCHERICHIA COLI

Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:X (auth: AX)
Chain Length:14
Number of Molecules:1
Biological Source:ESCHERICHIA COLI

Polymer Type:polyribonucleotide
Molecule:A-SITE TRNA G24A TRP-TRNA TRP
Chain IDs:Y (auth: AY)
Chain Length:77
Number of Molecules:1
Biological Source:ESCHERICHIA COLI

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ELONGATION FACTOR TU
Gene (Uniprot):tufB
Chain IDs:Z (auth: AZ)
Chain Length:405
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60339 Pfam ID:PF00009, PF03144, PF03143

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L27
Gene (Uniprot):rpmA
Chain IDs:AA (auth: B0)
Chain Length:85
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L28
Gene (Uniprot):rpmB
Chain IDs:BA (auth: B1)
Chain Length:98
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpmC
Chain IDs:CA (auth: B2)
Chain Length:72
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L30
Gene (Uniprot):rpmD
Chain IDs:DA (auth: B3)
Chain Length:60
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L31
Gene (Uniprot):rpmE
Chain IDs:EA (auth: B4)
Chain Length:71
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L32
Gene (Uniprot):rpmF
Chain IDs:FA (auth: B5)
Chain Length:60
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L33
Gene (Uniprot):rpmG
Chain IDs:GA (auth: B6)
Chain Length:54
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L34
Gene (Uniprot):rpmH
Chain IDs:HA (auth: B7)
Chain Length:49
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L35
Gene (Uniprot):rpmI
Chain IDs:IA (auth: B8)
Chain Length:65
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SKU1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L36
Gene (Uniprot):rpmJ
Chain IDs:JA (auth: B9)
Chain Length:37
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHR2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:KA (auth: BA)
Chain Length:2915
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:LA (auth: BB)
Chain Length:122
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L1
Gene (Uniprot):rplA
Chain IDs:MA (auth: BC)
Chain Length:229
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP7 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L2
Gene (Uniprot):rplB
Chain IDs:NA (auth: BD)
Chain Length:276
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L3
Gene (Uniprot):rplC
Chain IDs:OA (auth: BE)
Chain Length:206
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L4
Gene (Uniprot):rplD
Chain IDs:PA (auth: BF)
Chain Length:210
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L5
Gene (Uniprot):rplE
Chain IDs:QA (auth: BG)
Chain Length:182
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L6
Chain IDs:RA (auth: BH)
Chain Length:180
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L10
Chain IDs:SA (auth: BJ)
Chain Length:130
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L11
Chain IDs:TA (auth: BK)
Chain Length:140
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L13
Gene (Uniprot):rplM
Chain IDs:UA (auth: BN)
Chain Length:140
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L14
Gene (Uniprot):rplN
Chain IDs:VA (auth: BO)
Chain Length:122
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L15
Gene (Uniprot):rplO
Chain IDs:WA (auth: BP)
Chain Length:150
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L16
Gene (Uniprot):rplP
Chain IDs:XA (auth: BQ)
Chain Length:141
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L17
Gene (Uniprot):rplQ
Chain IDs:YA (auth: BR)
Chain Length:118
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L18
Gene (Uniprot):rplR
Chain IDs:ZA (auth: BS)
Chain Length:112
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L19
Gene (Uniprot):rplS
Chain IDs:AB (auth: BT)
Chain Length:146
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L20
Gene (Uniprot):rplT
Chain IDs:BB (auth: BU)
Chain Length:118
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L21
Gene (Uniprot):rplU
Chain IDs:CB (auth: BV)
Chain Length:101
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L22
Gene (Uniprot):rplV
Chain IDs:DB (auth: BW)
Chain Length:113
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L23
Gene (Uniprot):rplW
Chain IDs:EB (auth: BX)
Chain Length:96
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L24
Gene (Uniprot):rplX
Chain IDs:FB (auth: BY)
Chain Length:110
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L25
Gene (Uniprot):rplY
Chain IDs:GB (auth: BZ)
Chain Length:206
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
4SU	Y	U	4-THIOURIDINE-5'-MONOPHOSPHATE
5MU	Y	U	5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG	Y	G	MODIFIED GUANOSINE-5'-MONOPHOSPHATE
H2U	Y	U	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
MIA	Y	A	MODIFIED ADENOSINE-5'-MONOPHOSPHATE
OMC	Y	C	O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
PSU	Y	U	PSEUDOURIDINE-5'-MONOPHOSPHATE

Ligand Molecules

GCP

PAR

Primary Citation

The Mechanism for Activation of GTP Hydrolysis on the Ribosome.

Voorhees, R.M, Schmeing, T.M, Kelley, A.C, Ramakrishnan, V.Show

Science 330 835 ? (2010)

PMID: 21051640 DOI: 10.1126/SCIENCE.1194460

Abstact

Protein synthesis requires several guanosine triphosphatase (GTPase) factors, including elongation factor Tu (EF-Tu), which delivers aminoacyl-transfer RNAs (tRNAs) to the ribosome. To understand how the ribosome triggers GTP hydrolysis in translational GTPases, we have determined the crystal structure of EF-Tu and aminoacyl-tRNA bound to the ribosome with a GTP analog, to 3.2 angstrom resolution. EF-Tu is in its active conformation, the switch I loop is ordered, and the catalytic histidine is coordinating the nucleophilic water in position for inline attack on the γ-phosphate of GTP. This activated conformation is due to a critical and conserved interaction of the histidine with A2662 of the sarcin-ricin loop of the 23S ribosomal RNA. The structure suggests a universal mechanism for GTPase activation and hydrolysis in translational GTPases on the ribosome.

Legend

Protein

Chemical

Disease

Primary Citation of related structures