7QH6: 39S ribosomal protein L2, mitochondrial

Name: PDB 7QH6: Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 1
Published: 2022-03-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 1. Determined by electron microscopy at 3.08 Å resolution. Released 2 Mar 2022.

Method: Electron microscopy
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 46
Atoms: 83,425
Mol. weight: 1607.02 kDa
Ligands: ZN
Released: 2 Mar 2022

Explore 7QH6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QH6 contains 343 α-helices and 313 β-strands across 44 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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	89-94	6
α-helix	101-103	3
β-strand	107-110	4	92
β-strand	115-118	4	92
α-helix	124-145	22
β-strand	156-159	4	93
β-strand	173-176	4	93
α-helix	180-182	3

Chain 1: 0 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	15-20	6	94
β-strand	21	1	95
β-strand	30-35	6	94
β-strand	42-47	6	95
β-strand	52-57	6	95
β-strand	61-64	4	94

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-61	5
α-helix	66-69	4
α-helix	73-84	12

Chain 3: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4
β-strand	115-116	2	96
β-strand	122-124	3	96
α-helix	138-145	8
β-strand	148-149	2	96
α-helix	152-161	10
β-strand	172	1	36
α-helix	178-180	3

Chain 5: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	48-51	4
α-helix	56-58	3
β-strand	59	1	97
α-helix	60-62	3
β-strand	71	1	97
α-helix	75-78	4
α-helix	85-87	3
α-helix	90-92	3
β-strand	104-107	4	98
α-helix	117-124	8
β-strand	126-130	5	99
α-helix	134-137	4
α-helix	138-140	3
α-helix	150-162	13
α-helix	173-189	17
α-helix	190-193	4
α-helix	196-199	4
β-strand	201-204	4	99
β-strand	207-215	9	98
β-strand	218-226	9	98
β-strand	229-232	4	99
α-helix	235-238	4
α-helix	242-247	6
α-helix	248-250	3
β-strand	259	1	2
β-strand	266-268	3	98
β-strand	276	1	98
β-strand	287-294	8	99
α-helix	300-302	3
α-helix	306-329	24
β-strand	335-347	13	99
β-strand	352-361	10	99
β-strand	372-377	6	99
β-strand	385-387	3	100
β-strand	402-404	3	100
α-helix	409-419	11

Chain 6: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	50	1	83
α-helix	55-66	12
α-helix	75-78	4
α-helix	100-115	16
α-helix	117-124	8
α-helix	133-154	22
α-helix	157-162	6
β-strand	174-178	5	101
β-strand	184-187	4	101
β-strand	191-192	2	102
α-helix	196-198	3
α-helix	201-202	2
β-strand	203-205	3	101
β-strand	215-220	6	102
β-strand	231-237	7	102
β-strand	261	1	50
β-strand	266-275	10	102
β-strand	297-298	2	102
α-helix	300-306	7
β-strand	311-321	11	102
α-helix	325-329	5
α-helix	330-335	6
α-helix	338-339	2
β-strand	340-345	6	50
α-helix	346-350	5
α-helix	352-354	3
α-helix	363-367	5

Chain 7: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-69	6	6
β-strand	78-82	5	6
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	6
β-strand	111-114	4	6
α-helix	118-119	2
β-strand	124-128	5	6
α-helix	136-154	19
β-strand	164-168	5	7
α-helix	174-176	3
β-strand	179-185	7	7
α-helix	187-189	3
α-helix	196-212	17
β-strand	215	1	8
β-strand	217-222	6	9
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-256	6	9
β-strand	261-263	3	9
β-strand	271	1	8
β-strand	275-285	11	7
β-strand	294-303	10	7
α-helix	310-319	10

Chain 9: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	20-21	2
α-helix	28-33	6
α-helix	38-40	3
β-strand	42-45	4	14
β-strand	49-52	4	14
α-helix	54-56	3
β-strand	59-60	2	65
β-strand	73-74	2	78
α-helix	79-80	2
α-helix	88-103	16
β-strand	136	1	65

36 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	H	protein	267	Homo sapiens	Q9BYD2 (AlphaFold model)
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
39S ribosomal protein L18, mitochondrial	P	protein	180	Homo sapiens	Q9H0U6
39S ribosomal protein L19, mitochondrial	Q	protein	292	Homo sapiens	P49406
39S ribosomal protein L20, mitochondrial	R	protein	149	Homo sapiens	Q9BYC9

34 more molecules are not listed.

Sequence of entity 1 (D), FASTA

>7QH6_1 39S ribosomal protein L2, mitochondrial (chains D)
MALCALTRALRSLNLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALN
ANFVSWKSRTKYTITPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDFLRFRPEETKSG
PFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGD
AHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETC
VATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRKGGWAGRKIRPLPPMKSYVKLPS
ASAQS

Sequence of entity 2 (E), FASTA

>7QH6_2 39S ribosomal protein L3, mitochondrial (chains E)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Sequence of entity 3 (F), FASTA

>7QH6_3 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 4 (H), FASTA

>7QH6_4 39S ribosomal protein L9, mitochondrial (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 5 (K), FASTA

>7QH6_5 39S ribosomal protein L13, mitochondrial (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 6 (L), FASTA

>7QH6_6 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 7 (M), FASTA

>7QH6_7 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Sequence of entity 8 (N), FASTA

>7QH6_8 39S ribosomal protein L16, mitochondrial (chains N)
MWRLLARASAPLLRVPLSDSWALLPASAGVKTLLPVPSFEDVSIPEKPKLRFIERAPLVP
KVRREPKNLSDIRGPSTEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFA
IWRVPAPFKPITRKSVGHRMGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEVQGFLDQVA
HKLPFAAKAVSRGTLEKMRKDQEERERNNQNPWTFERIATANMLGIRKVLSPYDLTHKGK
YWGKFYMPKRV

Sequence of entity 9 (O), FASTA

>7QH6_9 39S ribosomal protein L17, mitochondrial (chains O)
MRLSVAAAISHGRVFRRMGLGPESRIHLLRNLLTGLVRHERIEAPWARVDEMRGYAEKLI
DYGKLGDTNERAMRMADFWLTEKDLIPKLFQVLAPRYKDQTGGYTRMLQIPNRSLDRAKM
AVIEYKGNCLPPLPLPRRDSHLTLLNQLLQGLRQDLRQSQEASNHSSHTAQTPGI

Sequence of entity 10 (P), FASTA

>7QH6_10 39S ribosomal protein L18, mitochondrial (chains P)
MALRSRFWGLFSVCRNPGCRFAALSTSSEPAAKPEVDPVENEAVAPEFTNRNPRNLELLS
VARKERGWRTVFPSREFWHRLRVIRTQHHVEALVEHQNGKVVVSASTREWAIKKHLYSTR
NVVACESIGRVLAQRCLEAGINFMVYQPTPWEAASDSMKRLQSAMTEGGVVLREPQRIYE

Sequence of entity 11 (Q), FASTA

>7QH6_11 39S ribosomal protein L19, mitochondrial (chains Q)
MAACIAAGHWAAMGLGRSFQAARTLLPPPASIACRVHAGPVRQQSTGPSEPGAFQPPPKP
VIVDKHRPVEPERRFLSPEFIPRRGRTDPLKFQIERKDMLERRKVLHIPEFYVGSILRVT
TADPYASGKISQFLGICIQRSGRGLGATFILRNVIEGQGVEICFELYNPRVQEIQVVKLE
KRLDDSLLYLRDALPEYSTFDVNMKPVVQEPNQKVPVNELKVKMKPKPWSKRWERPNFNI
KGIRFDLCLTEQQMKEAQKWNQPWLEFDMMREYDTSKIEAAIWKEIEASKRS

Sequence of entity 12 (R), FASTA

>7QH6_12 39S ribosomal protein L20, mitochondrial (chains R)
MVFLTAQLWLRNRVTDRYFRIQEVLKHARHFRGRKNRCYRLAVRTVIRAFVKCTKARYLK
KKNMRTLWINRITAASQEHGLKYPALIGNLVKCQVELNRKVLADLAIYEPKTFKSLAALA
SRRRHEGFAAALGDGKEPEGIFSRVVQYH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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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