7CPV: 80S ribosome from mouse testis

Name: PDB 7CPV: Cryo-EM structure of 80S ribosome from mouse testis
Published: 2022-02-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of 80S ribosome from mouse testis. Determined by electron microscopy at 3.03 Å resolution. Released 2 Feb 2022.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Mus musculus
Chains: 78
Atoms: 206,030
Mol. weight: 3679.38 kDa
Ligands: ZN, MG
Released: 2 Feb 2022

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

Secondary structure: helices and β-sheets

7CPV contains 476 α-helices and 547 β-strands across 73 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 La: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-9	3
α-helix	42-48	7
β-strand	72-73	2	176
α-helix	76-78	3
α-helix	84-90	7
β-strand	98	1	81
β-strand	100-102	3	177
α-helix	103-106	4
β-strand	110-111	2	176
β-strand	123-126	4	177
β-strand	128-129	2	176
α-helix	131-139	9
β-strand	143-146	4	177

Chain LA: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	10-12	3
β-strand	18	1	1
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-50	11	2
α-helix	51	1
β-strand	57-64	8	2
β-strand	71-77	7	2
β-strand	79	1	3
β-strand	83	1	4
β-strand	87-91	5	2
β-strand	101-103	3	2
α-helix	104-106	3
β-strand	112-113	2	5
β-strand	116	1	6
β-strand	126	1	6
β-strand	134-140	7	5
β-strand	145-149	5	5
β-strand	155-159	5	5
β-strand	163-165	3	2
β-strand	166	1	5
β-strand	169	1	3
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	1
β-strand	224-225	2	7
α-helix	229-230	2
β-strand	237-238	2	7

Chain Lb: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	22-26	5
α-helix	37-48	12
α-helix	54-65	12
α-helix	92-98	7
α-helix	104-112	9

Chain LB: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	32-34	3
β-strand	42-43	2	12
β-strand	45-59	15	13
β-strand	60	1	14
β-strand	68	1	14
β-strand	71-80	10	13
α-helix	82-83	2
β-strand	84-95	12	15
β-strand	98-106	9	15
α-helix	107	1
α-helix	112-115	4
α-helix	116-118	3
α-helix	131-134	4
α-helix	135-137	3
α-helix	140-156	17
β-strand	159-165	7	15
α-helix	168-170	3
α-helix	177-179	3
β-strand	180-184	5	15
β-strand	185-186	2	12
α-helix	190-200	11
β-strand	204-205	2	15
α-helix	207-210	4
β-strand	216-222	7	13
α-helix	223-225	3
β-strand	227-229	3	16
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-272	3	16
β-strand	276-288	13	13
β-strand	292-293	2	17
β-strand	297-298	2	17
β-strand	320	1	18
β-strand	324	1	18
β-strand	330-334	5	13
β-strand	344-349	6	13
β-strand	365-368	4	13
α-helix	382-389	8
α-helix	393-396	4

Chain Lc: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	14-18	5
β-strand	26-29	4	19
α-helix	31-39	9
β-strand	45-48	4	19
α-helix	54-67	14
β-strand	70-73	4	19
α-helix	78-84	7
β-strand	93-98	6	19

Chain LC: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	22
β-strand	17-23	7	22
α-helix	24-25	2
α-helix	26-29	4
α-helix	34-44	11
β-strand	65	1	23
β-strand	78	1	23
β-strand	90	1	23
α-helix	100-101	2
α-helix	117-131	15
α-helix	134-139	6
β-strand	152-154	3	22
α-helix	158-160	3
α-helix	164-173	10
α-helix	177-185	9
β-strand	188-189	2	24
α-helix	190	1
α-helix	193-195	3
β-strand	201-202	2	24
β-strand	208-210	3	22
α-helix	217-220	4
β-strand	228-229	2	22
α-helix	237-240	4
β-strand	250-253	4	22
α-helix	254-258	5
α-helix	260-263	4
α-helix	279-282	4
α-helix	289-292	4
α-helix	296-299	4
α-helix	312-314	3
α-helix	322-328	7
α-helix	331-349	19

Chain Ld: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	25
α-helix	38-40	3
α-helix	41-56	16
β-strand	62-63	2	25
α-helix	66-72	7
β-strand	83-92	10	25
β-strand	102-109	8	25
β-strand	120-121	2	25

Chain LD: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	18-20	3
α-helix	21-24	4
α-helix	30-37	8
α-helix	38-40	3
β-strand	50-55	6	28
β-strand	60-68	9	28
β-strand	71-79	9	28
α-helix	83-85	3
α-helix	95-113	19
α-helix	134-135	2
α-helix	139-142	4
β-strand	143	1	29
β-strand	145-147	3	28
α-helix	158-169	12
β-strand	172	1	29
β-strand	183-184	2	30
β-strand	189-190	2	30
α-helix	194-199	6
α-helix	202-214	13
α-helix	216-222	7
α-helix	224-227	4
α-helix	228-230	3
α-helix	236-249	14
α-helix	268-272	5
α-helix	273-292	20

65 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
60S ribosomal protein L8	LA	protein	257	Mus musculus	P62918 (AlphaFold model)
60S ribosomal protein L3	LB	protein	403	Mus musculus	P27659 (AlphaFold model)
60S ribosomal protein L4	LC	protein	419	Mus musculus	Q9D8E6 (AlphaFold model)
60S ribosomal protein L5	LD	protein	297	Mus musculus	P47962 (AlphaFold model)
60S ribosomal protein L6	LE	protein	296	Mus musculus	P47911
60S ribosomal protein L7	LF	protein	270	Mus musculus	P14148
60S ribosomal protein L7a	LG	protein	266	Mus musculus	P12970
60S ribosomal protein L9	LH	protein	192	Mus musculus	P51410
60S ribosomal protein L10-like	LI	protein	214	Mus musculus	P86048
60S ribosomal protein L11	LJ	protein	178	Mus musculus	Q9CXW4
60S ribosomal protein L13	LL	protein	211	Mus musculus	P47963
60S ribosomal protein L14	LM	protein	217	Mus musculus	Q9CR57

66 more molecules are not listed.

Sequence of entity 1 (LA), FASTA

>7CPV_1 60S ribosomal protein L8 (chains LA)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 2 (LB), FASTA

>7CPV_2 60S ribosomal protein L3 (chains LB)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 3 (LC), FASTA

>7CPV_3 60S ribosomal protein L4 (chains LC)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVQLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMMNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVKKLEAAATA
LATKSEKVVPEKGTADKKPAVGKKGKKVDAKKQKPAGKKVVAKKPAEKKPTTEEKKPAA

Sequence of entity 4 (LD), FASTA

>7CPV_4 60S ribosomal protein L5 (chains LD)
MGFVKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVNGGEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 5 (LE), FASTA

>7CPV_5 60S ribosomal protein L6 (chains LE)
MAGEKAPDTKEKKPAAKKAGSDAAASRPRAAKVAKKVHPKGKKPKKAKPHCSRNPVLVRG
IGRYSRSAMYSRKALYKRKYSAAKTKVEKKKKKEKVLATVTKTVGGDKNGGTRVVKLRKM
PRYYPTEDVPRKLLSHGKKPFSQHVRRLRSSITPGTVLIILTGRHRGKRVVFLKQLDSGL
LLVTGPLVINRVPLRRTHQKFVIATSTKVDISDVKIPKHLTDAYFKKKQLRKPRHQEGEI
FDTEKEKYEITEQRKADQKAVDLQILPKIKAVPQLQGYLRSQFSLTNGMYPHKLVF

Sequence of entity 6 (LF), FASTA

>7CPV_6 60S ribosomal protein L7 (chains LF)
MEAVPEKKKKVATVPGTLKKKVPAGPKTLKKKVPAVPETLKKKRRNFAELKVKRLRKKFA
LKTLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGI
NGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRG
YGKINKKRIALTDNSLIARSLGKFGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRG
GMKKKTTHFVEGGDAGNREDQINRLIRRMN

Sequence of entity 7 (LG), FASTA

>7CPV_7 60S ribosomal protein L7a (chains LG)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGHLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG

Sequence of entity 8 (LH), FASTA

>7CPV_8 60S ribosomal protein L9 (chains LH)
MKTILSNQTVDIPENVEITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRTGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Sequence of entity 9 (LI), FASTA

>7CPV_9 60S ribosomal protein L10-like (chains LI)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDKVAAKRLIPDGCGVKYIPERGPLDKWRALHS

Sequence of entity 10 (LJ), FASTA

>7CPV_10 60S ribosomal protein L11 (chains LJ)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Sequence of entity 11 (LL), FASTA

>7CPV_11 60S ribosomal protein L13 (chains LL)
MAPSRNGMILKPHFHKDWQQRVDTWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVYKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 12 (LM), FASTA

>7CPV_12 60S ribosomal protein L14 (chains LM)
MVFRRYVEVGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIDARERKAKMTDFDRFKVMKAKKMRN
RIIKTEVKKLQRAAILKASPKKAAVAKAAIAAAAAAAAAKAKVPAKKATGPGKKAAGQKA
PAQKAAGQKAAPPAKGQKGQKTPAQKAPAPKAAGKKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	247

Primary citation

A male germ-cell-specific ribosome controls male fertility. Li, H., Huo, Y., He, X. et al. Nature (2022) 612:725-731. DOI 10.1038/s41586-022-05508-0 · PubMed

Other PDB entries of the same protein (UniProt P62918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9H4N 2.46 Å, RPL13 (eL13)-mutant 80S ribosome from mouse
31FX 2.54 Å, Mouse 80S ribosome, sgRNA control
31FY 2.57 Å, Mouse 80S ribosome, Gm10076 KO
9KDT 2.63 Å, Cryo-EM structure of 80S ribosome
9KDW 2.67 Å, Cryo-EM structure of 80S ribosome
9QOH 2.78 Å, Mouse Ribosome POST translocation state
9QQP 2.8 Å, Mouse Ribosome rotated-2 PRE state
7CPU 2.82 Å, Cryo-EM structure of 80S ribosome from mouse kidney
31FZ 2.89 Å, Mouse 80S ribosome, eL41 KO
9KDU 2.96 Å, Cryo-EM structure of 80S ribosome
9QQL 3.09 Å, Mouse RPS15 P131 Mutant Ribosome POST translocation state
6SWA 3.1 Å, Mus musculus brain neocortex ribosome 60S bound to Ebp1

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