4V4B: Elongation factor 2

Name: PDB 4V4B: Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. Determined by electron microscopy at 11.7 Å resolution. Released 9 Jul 2014.

Method: Electron microscopy
Resolution: 11.7 Å
Organism: Saccharomyces cerevisiae
Chains: 47
Atoms: 146,792
Mol. weight: 2305.21 kDa
Released: 9 Jul 2014

Explore 4V4B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V4B contains 220 α-helices and 323 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 AB: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	30-35	6
β-strand	36-39	4	20
α-helix	41-43	3
β-strand	45-47	3	20
α-helix	49-65	17
β-strand	72-75	4	21
α-helix	79-90	12
β-strand	96-97	2	21
α-helix	115-117	3
β-strand	119-122	4	21
α-helix	129-138	10
β-strand	142-146	5	21
α-helix	152-154	3
β-strand	157-160	4	21
α-helix	166-184	19
α-helix	192-196	5

Chain AC: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-27	18
β-strand	33-37	5	24
β-strand	40	1	25
β-strand	45	1	25
β-strand	48-51	4	24
α-helix	54-58	5
α-helix	60-62	3
α-helix	63-75	13
β-strand	83	1	25
β-strand	86-89	4	24
α-helix	90	1
α-helix	93-95	3
α-helix	97-110	14
α-helix	114-127	14
β-strand	132-137	6	26
α-helix	141-143	3
β-strand	149	1	26
β-strand	152-154	3	26
β-strand	167-172	6	26
β-strand	183-188	6	26

Chain AD: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	23-30	8
α-helix	54-56	3
α-helix	57-72	16
α-helix	76-88	13
β-strand	92	1	30
α-helix	93-98	6
α-helix	105-107	3
β-strand	108	1	31
α-helix	109-116	8
α-helix	122-131	10
β-strand	134	1	32
β-strand	135-136	2	33
β-strand	139-140	2	33
α-helix	146	1
β-strand	147	1	31
α-helix	148-149	2
β-strand	152-153	2	34
α-helix	155	1
β-strand	156	1	32
α-helix	157	1
β-strand	176-179	4	34
β-strand	184-187	4	34

Chain AE: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	76-83	8	38
β-strand	88-89	2	39
β-strand	92-93	2	39
β-strand	97-104	8	38
β-strand	110-117	8	38
α-helix	120-132	13
β-strand	135-136	2	38
β-strand	156	1	40
β-strand	157-161	5	41
β-strand	164-170	7	41
β-strand	174	1	30
β-strand	177-178	2	41
α-helix	181-190	10
β-strand	195-201	7	41
α-helix	205-210	6
α-helix	211-219	9

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	78-81	4
α-helix	83-85	3
α-helix	91-100	10
α-helix	106-123	18
α-helix	128-139	12
β-strand	143-149	7	44
β-strand	154-160	7	44
α-helix	163-180	18
α-helix	190-200	11
α-helix	208-219	12

Chain AH: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	25-28	4	49
α-helix	31-43	13
β-strand	48-54	7	49
β-strand	57-63	7	49
β-strand	77-79	3	50
β-strand	88-89	2	50
β-strand	96	1	40
β-strand	100-105	6	50
β-strand	108-111	4	50
α-helix	112-118	7
β-strand	122-128	7	50

Chain AI: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	52
β-strand	11	1	52
β-strand	16-21	6	52
β-strand	28-30	3	52
β-strand	33-34	2	52
α-helix	35-38	4
α-helix	46-48	3
α-helix	49-53	5
α-helix	57	1
β-strand	64-69	6	52
α-helix	73-91	19
α-helix	125-127	3
α-helix	137-139	3

Chain AJ: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	55
β-strand	24-28	5	56
α-helix	31-45	15
β-strand	49	1	57
β-strand	61-66	6	58
β-strand	81-86	6	58
β-strand	87-89	3	56
β-strand	93	1	55
β-strand	96	1	57
α-helix	99-106	8
β-strand	112-116	5	56

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
18S ribosomal RNA	AA	RNA	1507	Saccharomyces cerevisiae
Elongation factor 2	AT	protein	842	Saccharomyces cerevisiae	P32324 (AlphaFold model)
40S ribosomal protein S0-A	AB	protein	185	Saccharomyces cerevisiae	P32905 (AlphaFold model)
40S ribosomal protein S3	AC	protein	192	Saccharomyces cerevisiae	P05750 (AlphaFold model)
40S ribosomal protein S9-A	AD	protein	179	Saccharomyces cerevisiae	O13516 (AlphaFold model)
40S ribosomal protein S2	AE	protein	149	Saccharomyces cerevisiae	P25443
40S ribosomal protein S5	AG	protein	150	Saccharomyces cerevisiae	P26783
40S ribosomal protein S22	AH	protein	129	Saccharomyces cerevisiae	P04648
40S ribosomal protein S16	AI	protein	142	Saccharomyces cerevisiae	P40213
40S ribosomal protein S20	AJ	protein	100	Saccharomyces cerevisiae	P38701
40S ribosomal protein S14-A	AK	protein	136	Saccharomyces cerevisiae	P06367
40S ribosomal protein S23	AL	protein	118	Saccharomyces cerevisiae	P32827

35 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V4B_1 18S ribosomal RNA (chains AA)
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCG
UGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGA
CCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGC
CCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCU
AGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCG
GCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUC
CGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGU
AAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGC
GCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUU
CACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCA
ACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCC
GGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUG
GUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGU
AGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACG
CGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGG
GGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAG
GCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAG
CACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAA
CGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCC
CGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGC
GACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCG
CAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCG
CUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGC
CCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCG
AGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGC
UGGAUCA

Sequence of entity 2 (AT), FASTA

>4V4B_2 Elongation factor 2 (chains AT)
MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTR
KDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALR
VTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFAR
TVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKM
MDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLL
EKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGP
ADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVP
GKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKV
MKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEI
CLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLA
IENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIK
DSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLA
DPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGF
TGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYD
KL

Sequence of entity 3 (AB), FASTA

>4V4B_3 40S ribosomal protein S0-A (chains AB)
AQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAARIIAAIPNPEDV
VAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLVIVTDPRSDAQAI
KEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREVLRLRGALVDRTQ
PWSIM

Sequence of entity 4 (AC), FASTA

>4V4B_4 40S ribosomal protein S3 (chains AC)
VALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGE
NGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYG
VVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGV
LGIKVKIMRDPA

Sequence of entity 5 (AD), FASTA

>4V4B_5 40S ribosomal protein S9-A (chains AD)
YESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIR
RLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGK
QIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEASGEAADEADEADEE

Sequence of entity 6 (AE), FASTA

>4V4B_6 40S ribosomal protein S2 (chains AE)
GLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKL
SVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVE
DVYTQSNGKTRTLENTLKAAFVAIGNTYG

Sequence of entity 7 (AG), FASTA

>4V4B_7 40S ribosomal protein S5 (chains AG)
RYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVD
AITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLA
EELINAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 8 (AH), FASTA

>4V4B_8 40S ribosomal protein S22 (chains AH)
TRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGKI
VVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGYVILTTSAGIMDHEEARRKHV
SGKILGFVY

Sequence of entity 9 (AI), FASTA

>4V4B_9 40S ribosomal protein S16 (chains AI)
SAVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFS
NIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIADS
RRPEPKKFGGKGARSRFQKSYR

Sequence of entity 10 (AJ), FASTA

>4V4B_10 40S ribosomal protein S20 (chains AJ)
KIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPTKVLKISTRKTPNGEGSKTWE
TYEMRIHKRYIDLEAPVQIVKRITQITIEPGVDVEVVASN

Sequence of entity 11 (AK), FASTA

>4V4B_11 40S ribosomal protein S14-A (chains AK)
SNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAM
LAAQDVAAKCREVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPV
PSDSTRKKGGRRGRRL

Sequence of entity 12 (AL), FASTA

>4V4B_12 40S ribosomal protein S23 (chains AL)
NYKKRLLGTAFKSSPFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFV
PNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS

Primary citation

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. Spahn, C.M., Gomez-Lorenzo, M.G., Grassucci, R.A. et al. EMBO J (2004) 23:1008-1019. DOI 10.1038/sj.emboj.7600102 · PubMed

Other PDB entries of the same protein (UniProt P32324 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
1N0U 2.12 Å, Crystal structure of yeast elongation factor 2 in complex with sordarin
3B82 2.35 Å, Structure of the eEF2-ExoA(E546H)-NAD+ complex
3B78 2.5 Å, Structure of the eEF2-ExoA(R551H)-NAD+ complex
3B8H 2.5 Å, Structure of the eEF2-ExoA(E546A)-NAD+ complex
8EUB 2.52 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
1U2R 2.6 Å, Crystal Structure of ADP-ribosylated Ribosomal Translocase from Saccharomyces cerevisiae
8EVS 2.62 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8EVQ 2.72 Å, Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I
1ZM9 2.8 Å, Structure of eEF2-ETA in complex with PJ34
1N0V 2.85 Å, Crystal structure of elongation factor 2
8T3A 2.86 Å, Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry…

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