7A5J: 39S ribosomal protein L2, mitochondrial

Name: PDB 7A5J: Structure of the split human mitoribosomal large subunit with P-and E-site mt-tRNAs
Published: 2020-12-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the split human mitoribosomal large subunit with P-and E-site mt-tRNAs. Determined by electron microscopy at 3.1 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Thermus thermophilus HB27
Chains: 63
Atoms: 106,132
Mol. weight: 1898.32 kDa
Ligands: MG, ZN
Released: 23 Dec 2020

Explore 7A5J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A5J contains 421 α-helices and 413 β-strands across 58 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 0: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
α-helix	87-94	8
α-helix	101-104	4
β-strand	107-109	3	121
β-strand	116-118	3	121
α-helix	124-145	22
β-strand	156-159	4	122
β-strand	173-176	4	122
α-helix	180-182	3

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	125
β-strand	29-35	7	125
β-strand	42-47	6	125
β-strand	52-64	13	125

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-64	8
α-helix	66-69	4
α-helix	73-85	13

Chain 3: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4
β-strand	114-116	3	131
β-strand	122-125	4	131
α-helix	126	1
α-helix	133-135	3
α-helix	138-144	7
β-strand	147-149	3	131
α-helix	152-161	10
α-helix	164-166	3
β-strand	172	1	63

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68	1	7
β-strand	80-84	5	7
β-strand	87-91	5	7
α-helix	96-98	3
β-strand	100-101	2	7

Chain 5: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
α-helix	48-50	3
β-strand	59	1	13
β-strand	71	1	13
α-helix	72-74	3
α-helix	85-87	3
α-helix	90-92	3
α-helix	103	1
β-strand	104-107	4	14
α-helix	117-124	8
β-strand	126-130	5	15
α-helix	134-137	4
α-helix	150-162	13
α-helix	173-188	16
α-helix	189-192	4
α-helix	196-200	5
β-strand	201-204	4	15
β-strand	207	1	16
β-strand	210-215	6	14
β-strand	218-223	6	14
β-strand	226	1	16
β-strand	229-232	4	15
α-helix	236-238	3
α-helix	242-245	4
α-helix	246-248	3
β-strand	259	1	5
β-strand	266-268	3	14
β-strand	276	1	14
β-strand	279	1	17
β-strand	287-292	6	15
α-helix	300-302	3
α-helix	304-305	2
α-helix	306-328	23
β-strand	335-347	13	15
β-strand	351-361	11	15
β-strand	372-381	10	15
β-strand	385-387	3	18
β-strand	391	1	19
β-strand	399	1	19
β-strand	402-404	3	18
α-helix	409-416	8

Chain 6: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	50	1	110
α-helix	55-66	12
α-helix	74-77	4
α-helix	100-113	14
α-helix	119-124	6
α-helix	132-142	11
α-helix	144-154	11
α-helix	158-161	4
β-strand	173-174	2	23
β-strand	175-178	4	24
β-strand	183	1	25
β-strand	184-187	4	24
β-strand	191-192	2	26
α-helix	201-202	2
β-strand	205-206	2	23
β-strand	214-220	7	26
β-strand	231-240	10	26
β-strand	249-252	4	26
α-helix	255-257	3
α-helix	259-260	2
β-strand	261	1	27
β-strand	266-275	10	26
α-helix	293-296	4
β-strand	297-298	2	26
α-helix	300-307	8
β-strand	311-315	5	26
β-strand	318-321	4	26
α-helix	326-329	4
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	27
α-helix	346-350	5
α-helix	353-355	3
β-strand	362	1	131
α-helix	363-369	7

Chain 7: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-69	6	35
β-strand	78-82	5	35
α-helix	88-95	8
α-helix	98-101	4
β-strand	103-108	6	35
β-strand	111-113	3	35
α-helix	118-119	2
β-strand	124-129	6	35
α-helix	136-155	20
β-strand	164-168	5	36
β-strand	179-185	7	36
α-helix	187-189	3
α-helix	196-211	16
β-strand	215	1	37
β-strand	219-222	4	38
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-256	6	38
β-strand	261-263	3	38
β-strand	271	1	37
β-strand	275-285	11	36
β-strand	295-303	9	36
α-helix	310-318	9

50 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
39S ribosomal protein L2, mitochondrial	D	protein	305	Homo sapiens	Q5T653 (AlphaFold model)
39S ribosomal protein L3, mitochondrial	E	protein	348	Homo sapiens	P09001 (AlphaFold model)
39S ribosomal protein L4, mitochondrial	F	protein	311	Homo sapiens	Q9BYD3 (AlphaFold model)
39S ribosomal protein L9, mitochondrial	C, H	protein	267	Homo sapiens	Q9BYD2 (AlphaFold model)
39S ribosomal protein L10, mitochondrial	I	protein	261	Homo sapiens	Q7Z7H8
39S ribosomal protein L11, mitochondrial	J	protein	192	Homo sapiens	Q9Y3B7
39S ribosomal protein L13, mitochondrial	K	protein	178	Homo sapiens	Q9BYD1
39S ribosomal protein L14, mitochondrial	L	protein	145	Homo sapiens	Q6P1L8
39S ribosomal protein L15, mitochondrial	M	protein	296	Homo sapiens	Q9P015
39S ribosomal protein L16, mitochondrial	N	protein	251	Homo sapiens	Q9NX20
39S ribosomal protein L17, mitochondrial	O	protein	175	Homo sapiens	Q9NRX2
Mitochondrial ribosomal protein L18, isoform CRA_b	P	protein	179	Homo sapiens	Q9H0U6

49 more molecules are not listed.

Sequence of entity 1 (D), FASTA

>7A5J_1 39S ribosomal protein L2, mitochondrial (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 2 (E), FASTA

>7A5J_2 39S ribosomal protein L3, mitochondrial (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 3 (F), FASTA

>7A5J_3 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 4 (C, H), FASTA

>7A5J_4 39S ribosomal protein L9, mitochondrial (chains C, H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 5 (I), FASTA

>7A5J_5 39S ribosomal protein L10, mitochondrial (chains I)
MAAAVAGMLRGGLLPQAGRLPTLQTVRYGSKAVTRHRRVMHFQRQKLMAVTEYIPPKPAI
HPSCLPSPPSPPQEEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHK
ILMKVFPNQVLKPFLEDSKYQNLLPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGC
IDDTILSRQGFINYSKLPSLPLVQGELVGGLTCLTAQTHSLLQHQPLQLTTLLDQYIREQ
REKDSVMSANGKPDPDTVPDS

Sequence of entity 6 (J), FASTA

>7A5J_6 39S ribosomal protein L11, mitochondrial (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 7 (K), FASTA

>7A5J_7 39S ribosomal protein L13, mitochondrial (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 8 (L), FASTA

>7A5J_8 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 9 (M), FASTA

>7A5J_9 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 10 (N), FASTA

>7A5J_10 39S ribosomal protein L16, mitochondrial (chains N)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Sequence of entity 11 (O), FASTA

>7A5J_11 39S ribosomal protein L17, mitochondrial (chains O)
MRLSVAAAISHGRVFRRMGLGPESRIHLLRNLLTGLVRHERIEAPWARVDEMRGYAEKLI
DYGKLGDTNERAMRMADFWLTEKDLIPKLFQVLAPRYKDQTGGYTRMLQIPNRSLDRAKM
AVIEYKGNCLPPLPLPRRDSHLTLLNQLLQGLRQDLRQSQEASNHSSHTAQTPGI

Sequence of entity 12 (P), FASTA

>7A5J_12 Mitochondrial ribosomal protein L18, isoform CRA_b (chains P)
MALRSQFWGFSVCRNPGCRFAALSTSSEPAAKPEVDPVENEAVAPEFTNRNPRNLELLSV
ARKERGWRTVFPSREFWHRLRVIRTQHHVEALVEHQNGKVVVSASTREWAIKKHLYSTRN
VVACESIGRVLAQRCLEAGINFMVYQPTPWEAASDSMKRLQSAMTEGGVVLREPQRIYE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	92
ZN	Zinc ion	Zn	3

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

Elongational stalling activates mitoribosome-associated quality control. Desai, N., Yang, H., Chandrasekaran, V. et al. Science (2020) 370:1105-1110. DOI 10.1126/science.abc7782 · PubMed

Other PDB entries of the same protein (UniProt Q5T653 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OF0 2.2 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
7QI4 2.21 Å, Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
8RRI 2.4 Å, Human mitochondrial ribosome in complex with antibiotic tigecycline
8QU5 2.42 Å, mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
7OF7 2.5 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
7PO4 2.56 Å, Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded…
6ZM6 2.59 Å, Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
7O9M 2.6 Å, Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4,…
7OF6 2.6 Å, Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6…
9CN3 2.62 Å, Human 39S mitoribosome in complex with antibiotic Linezolid
7QI5 2.63 Å, Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A…

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