National Center for
Biotechnology Information

6YDW: 55S mammalian mitochondrial ribosome with mtEFG1 and two tRNAMet (TI-POST)

PDB ID:

6YDW Download

MMDB ID:

192935

PDB Deposition Date:

2020/3/21

Updated in MMDB:

2024/10

Experimental Method:

electron microscopy

Resolution:

4.2 Å

Source Organism:

Sus scrofa▼

Taxonomy	Molecule
Sus scrofa	AI, BT, BU, BV, BW, BX, BY, Ba, Bb, Bc, Bd, Be, Bf, Bg, Bh, Bi, Bj, Bk, Bl, Bm, Bn, Bo, Bp, Bq, Bt, Bu, Bv, B0, Bw, Bx, AA, AB, AC, AE, AF, AG, AJ, AK, AL, AN, AO, AP, AQ, AR, AU, AZ, Aa, Ab, Ac, Ad, Ae, B1, Af, Ag, Ah, Ai, Aj, Ak, Am, An, Ao, Ap, CL, DL, EL, FL, GL, HL, LL, B2, B3, B4, B5, B6, B7, B8, B9, BA, BB, BD, BE, BF, BI, BJ, BK, BN, BO, BP, BQ, BR, BS
Homo sapiens	AV, AX, AY, BC

Similar Structures:

Biological Unit for 6YDW: 95-meric; determined by author

Molecular Components in 6YDW
Label	Count	Molecule
Proteins (89 molecules)
AI	1	Uncharacterized Protein
BT	1	Mitochondrial Ribosomal Protein L19
BU	1	Mitochondrial Ribosomal Protein L20
BV	1	Mitochondrial Ribosomal Protein L21
BW	1	Uncharacterized Protein
BX	1	Uncharacterized Protein
BY	1	Uncharacterized Protein
Ba	1	Mitochondrial Ribosomal Protein L37
Bb	1	Mitochondrial Ribosomal Protein L38
Bc	1	Mitochondrial Ribosomal Protein L39
Bd	1	Uncharacterized Protein
Be	1	Mitochondrial Ribosomal Protein L41
Bf	1	Uncharacterized Protein
Bg	1	Mitochondrial Ribosomal Protein L43
Bh	1	Uncharacterized Protein
Bi	1	Mitochondrial Ribosomal Protein L45
Bj	1	Mitochondrial Ribosomal Protein L46
Bk	1	39S Ribosomal Protein L48, Mitochondrial
Bl	1	Mrpl34
Bm	1	Mitochondrial Ribosomal Protein L50
Bn	1	Mitochondrial Ribosomal Protein L51
Bo	1	Uncharacterized Protein
Bp	1	Ml53
Bq	1	Uncharacterized Protein
Bt	1	Mitochondrial Ribosomal Protein L57
Bu	1	Uncharacterized Protein
Bv	1	Uncharacterized Protein
B0	1	Mitochondrial Ribosomal Protein L27
Bw	1	39S Ribosomal Protein S30, Mitochondrial
Bx	1	Mitochondrial Ribosomal Protein S18a
AB	1	Mitochondrial Ribosomal Protein S2
AC	1	Mitochondrial Ribosomal Protein S24
AE	1	Mitochondrial Ribosomal Protein S5
AF	1	Uncharacterized Protein
AG	1	Mitochondrial Ribosomal Protein S7
AJ	1	Mitochondrial Ribosomal Protein S10
AK	1	Us11m
AL	1	Mitochondrial Ribosomal Protein S12
AN	1	Mitochondrial Ribosomal Protein S14
AO	1	Us15m
AP	1	28S Ribosomal Protein S16, Mitochondrial
AQ	1	Us17m
AR	1	Mitochondrial Ribosomal Protein S18c
AU	1	Bs21m
AZ	1	Unknown Peptide
Aa	1	Mitochondrial Ribosomal Protein S22
Ab	1	Ms23
Ac	1	Mitochondrial Ribosomal Protein S25
Ad	1	Mitochondrial Ribosomal Protein S26
Ae	1	Mitochondrial Ribosomal Protein S27
B1	1	Mitochondrial Ribosomal Protein L28
Af	1	Mitoribosomal Protein Ms28, Mrps28
Ag	1	Death Associated Protein 3
Ah	1	Mitochondrial Ribosomal Protein S31
Ai	1	Ms33
Aj	1	Ms34
Ak	1	Mitochondrial Ribosomal Protein S35
Am	1	Ms37
An	1	Aurora Kinase a Interacting Protein 1
Ao	1	Ms39
Ap	1	28S Ribosomal Protein S18b, Mitochondrial
CL DL EL FL GL HL LL	7	Mitochondrial Ribosomal Protein L12
B2	1	Mitochondrial Ribosomal Protein L47
B3	1	Uncharacterized Protein
B4	1	Uncharacterized Protein
B5	1	Uncharacterized Protein
B6	1	Uncharacterized Protein
B7	1	Mitochondrial Ribosomal Protein L34
B8	1	Mitochondrial Ribosomal Protein L35
B9	1	Ribosomal Protein
BC	1	Elongation Factor G, Mitochondrial
BD	1	Uncharacterized Protein
BE	1	Ict1
BF	1	Mitochondrial Ribosomal Protein L4
BI	1	Mitochondrial Ribosomal Protein L9
BJ	1	Mitochondrial Ribosomal Protein L10
BK	1	Mitochondrial Ribosomal Protein L11
BN	1	Uncharacterized Protein
BO	1	Uncharacterized Protein
BP	1	Uncharacterized Protein
BQ	1	Uncharacterized Protein
BR	1	Uncharacterized Protein
BS	1	Mitochondrial Ribosomal Protein L18
Nucleotides(6 molecules)
AA BA	2	12S rRNA
AV AY	2	Trnamet
AX	1	mRNA
BB	1	CP tRNA-phe
Chemicals and Non-standard biopolymers (338 molecules)
1	325	MAGNESIUM ION
2	6	ZINC ION
3	3	SPERMINE
4	1	N-FORMYLMETHIONINE
5	1	GUANOSINE-5'-TRIPHOSPHATE
6	1	GUANOSINE-5'-MONOPHOSPHATE
7	1	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303