4V3P: G protein beta subunit

Name: PDB 4V3P: The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes
Published: 2015-04-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes. Determined by electron microscopy at 34.0 Å resolution. Released 22 Apr 2015.

Method: Electron microscopy
Resolution: 34.0 Å
Organism: Triticum aestivum
Chains: 87
Atoms: 195,694
Mol. weight: 3001.44 kDa
Released: 22 Apr 2015

Explore 4V3P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V3P contains 443 α-helices and 438 β-strands across 81 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: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	119
β-strand	44	1	119
α-helix	63-65	3
α-helix	66-96	31

Chain LA: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	11-12	2	78
α-helix	23-26	4
β-strand	34-40	7	78
β-strand	52-53	2	78
β-strand	56	1	79
β-strand	67-70	4	80
α-helix	74-81	8
β-strand	85-87	3	80
α-helix	89-91	3
α-helix	92-97	6
β-strand	104-107	4	80
α-helix	112-123	12
β-strand	136	1	80
α-helix	140-149	10
β-strand	151	1	79
β-strand	154-156	3	78
β-strand	161-168	8	78
α-helix	173-190	18
β-strand	202-205	4	78
β-strand	213-215	3	78

Chain Lb: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	74-75	2	145
β-strand	89-90	2	145
α-helix	95-106	12
α-helix	112-116	5
α-helix	119-127	9

Chain LB: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	6-9	4
β-strand	37	1	82
β-strand	42-51	10	83
β-strand	56-62	7	83
β-strand	75-77	3	83
α-helix	78	1
β-strand	79	1	84
β-strand	83	1	67
β-strand	87-89	3	83
β-strand	90	1	85
β-strand	101-103	3	85
α-helix	104-106	3
α-helix	108	1
β-strand	111-114	4	85
β-strand	116	1	86
β-strand	126	1	86
β-strand	134-138	5	85
β-strand	146-149	4	85
β-strand	155-158	4	85
β-strand	163-166	4	85
α-helix	168	1
β-strand	169	1	84
α-helix	182-190	9
β-strand	224-225	2	87
α-helix	230	1
β-strand	237-238	2	87

Chain Lc: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	8-12	5
α-helix	16-39	24
α-helix	42-74	33
α-helix	83-88	6
α-helix	91-95	5
α-helix	101-104	4
α-helix	119-122	4

Chain LC: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
β-strand	43	1	41
β-strand	45-58	14	42
β-strand	72-80	9	42
β-strand	84-93	10	43
α-helix	94	1
β-strand	96	1	44
β-strand	98	1	44
β-strand	100-106	7	43
α-helix	113-116	4
α-helix	134-137	4
α-helix	139-156	18
β-strand	159-166	8	43
α-helix	168-170	3
β-strand	180-185	6	43
β-strand	186	1	41
α-helix	191-202	12
β-strand	206	1	43
α-helix	208-210	3
β-strand	217-223	7	42
α-helix	224-225	2
β-strand	226-230	5	45
α-helix	232-236	5
α-helix	238-241	4
β-strand	271-274	4	45
β-strand	277-284	8	42
β-strand	287-290	4	42
α-helix	311	1
β-strand	315	1	46
β-strand	319	1	46
β-strand	324-329	6	42
β-strand	339-344	6	42
β-strand	360-363	4	42
β-strand	369	1	47
β-strand	371	1	47
α-helix	376-383	8

Chain Ld: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	39-48	10
α-helix	51-56	6

Chain LD: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	52
β-strand	12	1	53
β-strand	26-27	2	52
α-helix	28-29	2
α-helix	30-33	4
α-helix	38-50	13
α-helix	117-120	4
α-helix	121-134	14
α-helix	138-144	7
β-strand	156-158	3	53
α-helix	168-178	11
α-helix	181-185	5
β-strand	192-193	2	54
α-helix	197-200	4
β-strand	205-206	2	54
β-strand	212-215	4	53
α-helix	224-227	4
β-strand	233-236	4	53
α-helix	237-239	3
α-helix	242-245	4
α-helix	247-249	3
β-strand	255-258	4	53
α-helix	259-262	4
α-helix	307-313	7
α-helix	318-325	8
α-helix	333-340	8
α-helix	351-354	4
α-helix	358-383	26
α-helix	390-403	14

71 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
G protein beta subunit	Sa	protein	380	Triticum aestivum	Q8LNY6 (AlphaFold model)
40S ribosomal protein SA	SA	protein	260	Triticum aestivum
Putative 40S ribosomal protein S3	SB	protein	208	Triticum aestivum	Q8L804 (AlphaFold model)
40S ribosomal protein S4	SD	protein	200	Triticum aestivum
40S ribosomal protein S2	SE	protein	263	Triticum aestivum
40S ribosomal protein S5	SF	protein	191	Triticum aestivum
40S ribosomal protein S16	SI	protein	126	Triticum aestivum
40S ribosomal protein S20	SJ	protein	128	Triticum aestivum
40S ribosomal protein S14	SK	protein	119	Triticum aestivum
40S ribosomal protein S23	SL	protein	142	Triticum aestivum
40S ribosomal protein S18	SM	protein	152	Triticum aestivum
40S ribosomal protein S13-1	SO	protein	121	Triticum aestivum

72 more molecules are not listed.

Sequence of entity 1 (Sa), FASTA

>4V3P_1 G protein beta subunit (chains Sa)
MASVAELKEKHAAATASVNSLRERLRQRRQTLLDTDVEKYSKAQGRTAVSFNPTDLVCCR
TLQGHSGKVYSLDWTPEKNWIVSASQDGRLIVWNALTSQKTHAIKLHCPWVMECAFAPNG
QSVACGGLDSACSIFNLSSQADRDGNMPVSRVLTGHKGYASSCQYVPDQETRLITGSGDQ
TCVLWDVTTGQRISIFGSEFPSGHTADVLSLSINSLNANMFISGSCDTTVRLWDLRITSR
AVRTYHGHEGDINSVKFFPDGQRFGTGSDDGTCRLFDMRTGHQLQVYNREPDRNDNELPI
VTSVAFSISGRLLFAGYSNGDCYVWDTLLAEMVLNLGTLQNSHEGRISCLGLSSDGSALC
TGSWDKNLKIWAFSGHRKIV

Sequence of entity 2 (SA), FASTA

>4V3P_2 40S ribosomal protein SA (chains SA)
MAAEGGAAARALSQREQDIQMMLAADVHLGTKNCDFQMERYVYKRRTDGIYIINLGKTWE
KLQLAARVIVAIENPQDIIVQSARPYGQRAVLKFAQYTGAHAIAGRHTPGTFTNQLQTSF
SEPRLLILTDPRTDHQPIKESALGNIPTIAFCDTDSPMRYVDIGIPANNKGKQSIGCLFW
LLARMVLQMRGTILPGHKWDVMVDLFFYRDPEEAKEQEEEEAALVAPDYGAVAEYAAPAA
DTWGGEWGTDAAAQPAAIPA

Sequence of entity 3 (SB), FASTA

>4V3P_3 Putative 40S ribosomal protein S3 (chains SB)
VSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTS
VVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGA
KGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQGVLGIKVKIMLD
WDPKGKLGPTTPLPDLVTIHPPKEENEL

Sequence of entity 4 (SD), FASTA

>4V3P_4 40S ribosomal protein S4 (chains SD)
PLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLL
YDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKI
DLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRL
GNVFTIGKGNKPWVSLPKGK

Sequence of entity 5 (SE), FASTA

>4V3P_5 40S ribosomal protein S2 (chains SE)
MAERGGERGGERGGFGRGFGRGGRGDRGGRRGGRRGPRQEEEKWVPVTKLGRLVKEGRFS
KIEEIYLHSLPVKEHQIVETLVPGLKDEVMKITPVQKQTRAGQRTRFKAFVVVGDNNGHV
GLGVKCAKEVATAIRGAIILAKLSVVPVRRGYWGNKIGQPHTVPCKVTGKCGSVTVRMVP
APRGSGIVAARVPKKVLQFAGIEDVFTSSRGSTKTLGNFVKATFDCLMKTYGFLTPDFWR
DTKFVKSPFQEYTDLLAKPTKAL

Sequence of entity 6 (SF), FASTA

>4V3P_6 40S ribosomal protein S5 (chains SF)
QVVKLFNCWSFEDVQVNDISLADYLAVSSTKHATYLPHTAGRYSAKRFRKAQCPLVERLT
NSLMMHGRNNGKKIMAVRIVKHAMEIIHLLTDANPIQVIVDAIINSGPREDATRIGSAGA
VRRQAVDISPLRRVNQAIYLLTTGARESAFRNIKTIAECLADELINAAKGSSNSYAIKKK
DEIERVAKANR

Sequence of entity 7 (SI), FASTA

>4V3P_7 40S ribosomal protein S16 (chains SI)
AVSYCKPGRGLIKVNGVPIELIRPEMLRLKAFEPILLAGRSRFKDIDMRIRVRGGGKTSQ
IYAIRQAIAKALVAYYQKYVDEASKKEVKDIFARYDRTLLVADPRRCEPKKFGGRGARAR
FQKSYR

Sequence of entity 8 (SJ), FASTA

>4V3P_8 40S ribosomal protein S20 (chains SJ)
MAAADVAYAPPMKSGKIGFESSQEVQHRIRITLSSKSVKNLEKVCGDLVKGAKDKSLKVK
GPVRMPTKVLHITTRKSPCGEGTNTWDRFEMRVHKRVIDLVSSADVVKQITSITIEPGVE
VEVTISDQ

Sequence of entity 9 (SK), FASTA

>4V3P_9 40S ribosomal protein S14 (chains SK)
IFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLASQDVAQRCKELGITA
LHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPVPTDSTRRKGGRRGRRL

Sequence of entity 10 (SL), FASTA

>4V3P_10 40S ribosomal protein S23 (chains SL)
MGKTRGMGAGRKLKTHRRNQRWADKAYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQ
PNSAIRKCARVQLVKNGKKIAAFVPNDGCLNFIEENDEVLIAGFGRKGHAVGDIPGVRFK
VVKVSGVSLLALFKEKKEKPRS

Sequence of entity 11 (SM), FASTA

>4V3P_11 40S ribosomal protein S18 (chains SM)
MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELS
AEEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNH
RGLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR

Sequence of entity 12 (SO), FASTA

>4V3P_12 40S ribosomal protein S13-1 (chains SO)
ADVEEMIMKAAKKGQMPSQIGVVLRDQHGIPLVKSVTGSKILRILKAHGLAPEIPEDLYF
LIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKRTKKLPPTWKYESTTASTLV
A

Primary citation

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes. Myasnikov, A.G., Afonina, Z.A., Menetret, J.F. et al. Nat Commun (2014) 5:5294-5294. DOI 10.1038/ncomms6294 · PubMed

Other PDB entries of the same protein (UniProt Q8LNY6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4V7E 5.5 Å, Model of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum…

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