7QH7: 39S ribosomal protein L2, mitochondrial

Name: PDB 7QH7: Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4
Published: 2022-05-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4. Determined by electron microscopy at 2.89 Å resolution. Released 18 May 2022.

Method: Electron microscopy
Resolution: 2.89 Å
Organism: Homo sapiens
Chains: 49
Atoms: 85,397
Mol. weight: 1248.84 kDa
Ligands: MG, ZN
Released: 18 May 2022

Explore 7QH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QH7 contains 348 α-helices and 303 β-strands across 47 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: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
α-helix	87-94	8
α-helix	97-99	3
α-helix	101-104	4
β-strand	107-109	3	84
β-strand	116-118	3	84
α-helix	124-145	22
β-strand	156-159	4	85
α-helix	164-166	3
β-strand	173-176	4	85
α-helix	180-182	3

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	86
β-strand	30-35	6	86
β-strand	42-47	6	86
β-strand	52-61	10	86

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-63	7
α-helix	66-70	5
α-helix	73-84	12

Chain 3: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4
β-strand	115-116	2	88
β-strand	122-124	3	88
α-helix	138-144	7
β-strand	148-149	2	88
α-helix	152-160	9
α-helix	165-167	3
β-strand	172	1	42
α-helix	178-180	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-68	2	87
β-strand	79-84	6	87
β-strand	87-92	6	87
α-helix	96-98	3
β-strand	100-101	2	87

Chain 5: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	42-47	6
α-helix	48-51	4
β-strand	59	1	89
β-strand	71	1	89
α-helix	75-78	4
α-helix	85-87	3
α-helix	90-92	3
α-helix	93-95	3
β-strand	104-108	5	90
α-helix	117-124	8
β-strand	126-130	5	91
α-helix	134-137	4
α-helix	150-162	13
α-helix	173-188	16
β-strand	201-204	4	91
β-strand	207-215	9	90
β-strand	218-226	9	90
β-strand	229-232	4	91
α-helix	235-238	4
α-helix	242-245	4
α-helix	246-248	3
α-helix	252-254	3
β-strand	259	1	4
β-strand	266-268	3	90
β-strand	276	1	90
β-strand	287-294	8	91
α-helix	300-302	3
α-helix	306-328	23
β-strand	335-347	13	91
β-strand	351-361	11	91
α-helix	370-371	2
β-strand	372-381	10	91
β-strand	383-387	5	92
β-strand	402-406	5	92
α-helix	409-419	11

Chain 6: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
α-helix	34-35	2
α-helix	54-64	11
α-helix	74-77	4
α-helix	132-154	23
α-helix	158-161	4
β-strand	177-178	2	6
β-strand	184-185	2	6
β-strand	191-192	2	7
α-helix	195-198	4
β-strand	214-220	7	7
β-strand	231-237	7	7
β-strand	238	1	8
β-strand	239-240	2	7
β-strand	249	1	8
β-strand	261	1	9
β-strand	266-275	10	7
α-helix	293-296	4
β-strand	297-298	2	7
α-helix	300-306	7
β-strand	311-321	11	7
α-helix	328-329	2
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	9
α-helix	346-350	5
α-helix	352-355	4
β-strand	362	1	88
α-helix	365-368	4
α-helix	375-376	2

Chain 7: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-56	20
β-strand	64-69	6	14
β-strand	78-82	5	14
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	14
β-strand	112-113	2	14
α-helix	118-119	2
β-strand	123-128	6	14
α-helix	136-154	19
β-strand	165-168	4	15
α-helix	174-176	3
β-strand	179-184	6	15
α-helix	187-189	3
α-helix	193-195	3
α-helix	196-212	17
β-strand	215	1	16
β-strand	217-222	6	17
α-helix	225-228	4
α-helix	239-244	6
β-strand	251-256	6	17
β-strand	261-262	2	17
β-strand	271	1	16
β-strand	275-285	11	15
β-strand	294-303	10	15
α-helix	310-318	9

39 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	215	Homo sapiens	Q5T653 (AlphaFold model)
39S ribosomal protein L3, mitochondrial	E	protein	304	Homo sapiens	P09001 (AlphaFold model)
39S ribosomal protein L4, mitochondrial	F	protein	250	Homo sapiens	Q9BYD3 (AlphaFold model)
39S ribosomal protein L9, mitochondrial	H	protein	95	Homo sapiens	Q9BYD2 (AlphaFold model)
39S ribosomal protein L10, mitochondrial	I	protein	30	Homo sapiens	Q7Z7H8
39S ribosomal protein L13, mitochondrial	K	protein	177	Homo sapiens	Q9BYD1
39S ribosomal protein L14, mitochondrial	L	protein	115	Homo sapiens	Q6P1L8
39S ribosomal protein L15, mitochondrial	M	protein	287	Homo sapiens	Q9P015
39S ribosomal protein L16, mitochondrial	N	protein	201	Homo sapiens	Q9NX20
39S ribosomal protein L17, mitochondrial	O	protein	152	Homo sapiens	Q9NRX2
39S ribosomal protein L18, mitochondrial	P	protein	141	Homo sapiens	Q9H0U6
39S ribosomal protein L19, mitochondrial	Q	protein	217	Homo sapiens	P49406

37 more molecules are not listed.

Sequence of entity 1 (D), FASTA

>7QH7_1 39S ribosomal protein L2, mitochondrial (chains D)
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRW

Sequence of entity 2 (E), FASTA

>7QH7_2 39S ribosomal protein L3, mitochondrial (chains E)
SGTWWDEHLSEENVPFIKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKL
GMMPLWTKDGQKHVVTLLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEF
YRELGLPPKQTVKIFNITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGF
KGQPATHGQTKTHRRPGAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIY
VNGSVPGHKNCLVKVKDSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPS
ITFA

Sequence of entity 3 (F), FASTA

>7QH7_3 39S ribosomal protein L4, mitochondrial (chains F)
EPVLRKVELPVPTHRRPVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQK
NFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYM
LPMKVRALGLKVALTVKLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHE
EMPQSIVEATSRLKTFNLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLY
PFSLPYSDFP

Sequence of entity 4 (H), FASTA

>7QH7_4 39S ribosomal protein L9, mitochondrial (chains H)
TVIVERWWKVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLV
SVKKSLGRNRLLPQGLAVYASPENKKLFEEEKLLR

Sequence of entity 5 (I), FASTA

>7QH7_5 39S ribosomal protein L10, mitochondrial (chains I)
RRVMHFQRQKLMAVTEYIPPKPAIHPSCLP

Sequence of entity 6 (K), FASTA

>7QH7_6 39S ribosomal protein L13, mitochondrial (chains K)
SSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMN
TRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRTM
MERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 7 (L), FASTA

>7QH7_7 39S ribosomal protein L14, mitochondrial (chains L)
AIQKMTRVRVVDNSALGNSPYHRAPRCIHVYKKNGVGKVGDQILLAIKGQKKKALIVGHC
MPGPRMTPRFDSNNVVLIEDNGNPVGTRIKTPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 8 (M), FASTA

>7QH7_8 39S ribosomal protein L15, mitochondrial (chains M)
ARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRGTRPRLGFEG
GQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQLVNGRGVTI
QPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLDIVCK
PVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKYGYILPDITK
DELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 9 (N), FASTA

>7QH7_9 39S ribosomal protein L16, mitochondrial (chains N)
RFIERAPLVPKVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTIN
RSMDPKNMFAIWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFE
EVQGFLDQVAHKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVL
SPYDLTHKGKYWGKFYMPKRV

Sequence of entity 10 (O), FASTA

>7QH7_10 39S ribosomal protein L17, mitochondrial (chains O)
ISHGRVFRRMGLGPESRIHLLRNLLTGLVRHERIEAPWARVDEMRGYAEKLIDYGKLGDT
NERAMRMADFWLTEKDLIPKLFQVLAPRYKDQTGGYTRMLQIPNRSLDRAKMAVIEYKGN
CLPPLPLPRRDSHLTLLNQLLQGLRQDLRQSQ

Sequence of entity 11 (P), FASTA

>7QH7_11 39S ribosomal protein L18, mitochondrial (chains P)
VENEAVAPEFTNRNPRNLELLSVARKERGWRTVFPSREFWHRLRVIRTQHHVEALVEHQN
GKVVVSASTREWAIKKHLYSTRNVVACESIGRVLAQRCLEAGINFMVYQPTPWEAASDSM
KRLQSAMTEGGVVLREPQRIY

Sequence of entity 12 (Q), FASTA

>7QH7_12 39S ribosomal protein L19, mitochondrial (chains Q)
RFLSPEFIPRRGRTDPLKFQIERKDMLERRKVLHIPEFYVGSILRVTTADPYASGKISQF
LGICIQRSGRGLGATFILRNVIEGQGVEICFELYNPRVQEIQVVKLEKRLDDSLLYLRDA
LPEYSTFDVNMKPVVQEPNQKVPVNELKVKMKPKPWSKRWERPNFNIKGIRFDLCLTEQQ
MKEAQKWNQPWLEFDMMREYDTSKIEAAIWKEIEASK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	50
ZN	Zinc ion	Zn	3

Primary citation

A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit. Rebelo-Guiomar, P., Pellegrino, S., Dent, K.C. et al. Nat Commun (2022) 13:929-929. DOI 10.1038/s41467-022-28503-5 · 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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