7CPU: 80S ribosome from mouse kidney

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

Cryo-EM structure of 80S ribosome from mouse kidney. Determined by electron microscopy at 2.82 Å resolution. Released 2 Feb 2022.

Method: Electron microscopy
Resolution: 2.82 Å
Organism: Mus musculus
Chains: 78
Atoms: 206,288
Mol. weight: 3680.08 kDa
Ligands: MG, ZN
Released: 2 Feb 2022

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

Secondary structure: helices and β-sheets

7CPU contains 469 α-helices and 541 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: 5 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	72-74	3	15
α-helix	84-92	9
β-strand	98	1	93
β-strand	100-102	3	16
β-strand	110-112	3	15
β-strand	123-126	4	16
β-strand	128-129	2	15
α-helix	131-140	10
β-strand	143-146	4	16

Chain LA: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	10-12	3
α-helix	14-16	3
β-strand	18	1	1
α-helix	30-32	3
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
α-helix	78	1
β-strand	79	1	3
β-strand	83	1	4
β-strand	87-91	5	2
β-strand	101-103	3	2
β-strand	112-113	2	5
β-strand	116	1	6
β-strand	120	1	7
β-strand	122	1	7
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
α-helix	168	1
β-strand	169	1	3
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	1
α-helix	201-203	3
β-strand	224-225	2	8
α-helix	229-230	2
β-strand	237-238	2	8

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	54-68	15
α-helix	92-98	7
α-helix	104-114	11

Chain LB: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	40-41	2
β-strand	42-43	2	19
β-strand	45-59	15	20
β-strand	71-80	10	20
α-helix	82-83	2
β-strand	84-95	12	19
β-strand	98-106	9	19
α-helix	112-115	4
α-helix	116-118	3
α-helix	135-138	4
α-helix	142-156	15
β-strand	159-165	7	19
α-helix	168-170	3
β-strand	180-186	7	19
α-helix	190-200	11
β-strand	204-205	2	19
α-helix	207-210	4
β-strand	216-222	7	20
α-helix	223-224	2
β-strand	225-229	5	21
α-helix	231-235	5
α-helix	237-241	5
β-strand	270-273	4	21
β-strand	276-288	13	20
β-strand	292-293	2	22
β-strand	297-298	2	22
α-helix	300-302	3
β-strand	320	1	23
β-strand	324	1	23
β-strand	330-334	5	20
β-strand	344-349	6	20
β-strand	365-368	4	20
α-helix	382-389	8

Chain Lc: 4 helices, 4 β-strands

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

Chain LC: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	34
β-strand	17-23	7	34
α-helix	24-25	2
α-helix	26-29	4
α-helix	34-44	11
α-helix	45-48	4
β-strand	65	1	35
β-strand	78	1	35
β-strand	90	1	35
α-helix	117-131	15
α-helix	134-139	6
β-strand	152-154	3	34
α-helix	158-160	3
α-helix	164-174	11
α-helix	177-185	9
β-strand	188-189	2	36
α-helix	190	1
α-helix	193-195	3
β-strand	201-202	2	36
β-strand	208-210	3	34
α-helix	217-220	4
β-strand	228-229	2	34
α-helix	237-240	4
β-strand	250-253	4	34
α-helix	254-264	11
α-helix	279-282	4
α-helix	289-292	4
α-helix	296-299	4
α-helix	302-305	4
α-helix	311-313	3
α-helix	322-328	7
α-helix	331-349	19

Chain Ld: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	37
α-helix	29-32	4
α-helix	38-40	3
α-helix	41-56	16
β-strand	62-63	2	37
α-helix	66-72	7
β-strand	83-92	10	37
β-strand	102-105	4	37
β-strand	108-109	2	37
β-strand	120-121	2	37

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	49-55	7	39
β-strand	60-67	8	39
β-strand	72-79	8	39
α-helix	80-85	6
α-helix	95-113	19
α-helix	134-135	2
α-helix	139-142	4
β-strand	143	1	40
β-strand	145-147	3	39
α-helix	158-169	12
β-strand	172	1	40
β-strand	183-184	2	41
β-strand	189-190	2	41
α-helix	194-200	7
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	269-272	4
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)
40S ribosomal protein SA	SA	protein	295	Mus musculus	P14206 (AlphaFold model)
60S ribosomal protein L3	LB	protein	403	Mus musculus	P27659 (AlphaFold model)
40S ribosomal protein S3a	SB	protein	264	Mus musculus	P97351 (AlphaFold model)
60S ribosomal protein L4	LC	protein	419	Mus musculus	Q9D8E6
60S ribosomal protein L5	LD	protein	297	Mus musculus	P47962
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	LI	protein	214	Mus musculus	Q6ZWV3
60S ribosomal protein L11	LJ	protein	178	Mus musculus	Q9CXW4

66 more molecules are not listed.

Sequence of entity 1 (LA), FASTA

>7CPU_1 60S ribosomal protein L8 (chains LA)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 2 (SA), FASTA

>7CPU_2 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
AQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTEWS

Sequence of entity 3 (LB), FASTA

>7CPU_3 60S ribosomal protein L3 (chains LB)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 4 (SB), FASTA

>7CPU_4 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGGSSGK
AAGDETGAKVERADGYEPPVQESV

Sequence of entity 5 (LC), FASTA

>7CPU_5 60S ribosomal protein L4 (chains LC)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVQLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMMNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVKKLEAAATA
LATKSEKVVPEKGTADKKPAVGKKGKKVDAKKQKPAGKKVVAKKPAEKKPTTEEKKPAA

Sequence of entity 6 (LD), FASTA

>7CPU_6 60S ribosomal protein L5 (chains LD)
MGFVKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVNGGEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 7 (LE), FASTA

>7CPU_7 60S ribosomal protein L6 (chains LE)
MAGEKAPDTKEKKPAAKKAGSDAAASRPRAAKVAKKVHPKGKKPKKAKPHCSRNPVLVRG
IGRYSRSAMYSRKALYKRKYSAAKTKVEKKKKKEKVLATVTKTVGGDKNGGTRVVKLRKM
PRYYPTEDVPRKLLSHGKKPFSQHVRRLRSSITPGTVLIILTGRHRGKRVVFLKQLDSGL
LLVTGPLVINRVPLRRTHQKFVIATSTKVDISDVKIPKHLTDAYFKKKQLRKPRHQEGEI
FDTEKEKYEITEQRKADQKAVDLQILPKIKAVPQLQGYLRSQFSLTNGMYPHKLVF

Sequence of entity 8 (LF), FASTA

>7CPU_8 60S ribosomal protein L7 (chains LF)
MEAVPEKKKKVATVPGTLKKKVPAGPKTLKKKVPAVPETLKKKRRNFAELKVKRLRKKFA
LKTLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGI
NGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRG
YGKINKKRIALTDNSLIARSLGKFGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRG
GMKKKTTHFVEGGDAGNREDQINRLIRRMN

Sequence of entity 9 (LG), FASTA

>7CPU_9 60S ribosomal protein L7a (chains LG)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGHLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG

Sequence of entity 10 (LH), FASTA

>7CPU_10 60S ribosomal protein L9 (chains LH)
MKTILSNQTVDIPENVEITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRTGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Sequence of entity 11 (LI), FASTA

>7CPU_11 60S ribosomal protein L10 (chains LI)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 12 (LJ), FASTA

>7CPU_12 60S ribosomal protein L11 (chains LJ)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	271
ZN	Zinc ion	Zn	7

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
31FZ 2.89 Å, Mouse 80S ribosome, eL41 KO
9KDU 2.96 Å, Cryo-EM structure of 80S ribosome
7CPV 3.03 Å, Cryo-EM structure of 80S ribosome from mouse testis
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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