Structure of PDB 5jup Chain DC

Receptor sequence

>5jupDC (length=824) Species: 4932 (Saccharomyces cerevisiae)

VAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAGI
TIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAA
LRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQ
VSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGW
AFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKP
LERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKA
LLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIA
IKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNY
VPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGT
LTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCV
LTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVE
SESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARI
MADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQ
WATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFL
LADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTV
KAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEI
VLAARKRHGMKEEVPGWQEYYDKL

3D structure

• PDB: 5jup Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
• Chain: DC
• Resolution: 3.5 Å

Enzymatic activity

• Enzyme Commision number: 3.6.5.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	DC	K391 R393 K613 X699	K373 R375 K595 X681
BS02	rna	DC	H27 V28 H108 V137 R162 P580 G741 Y744 Q753 V754 R785 Q786 G789 G790	H26 V27 H90 V119 R144 P562 G723 Y726 Q735 V736 R767 Q768 G771 G772
BS03	rna	DC	H583 H694 D696 X699 L842	H565 H676 D678 X681 L824
BS04	GDP	DC	V28 D29 G31 K32 S33 T34 N158 K159 D161 S213 L215	V27 D28 G30 K31 S32 T33 N140 K141 D143 S195 L197
BS05	MG	DC	S33 T69	S32 T51
BS06	SO1	DC	Y521 S523 P559 V561 A562 P727 F798 W801	Y503 S505 P541 V543 A544 P709 F780 W783

Gene Ontology

Molecular Function

• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0019843 rRNA binding
• GO:0042802 identical protein binding
• GO:0043022 ribosome binding
• GO:0051087 protein-folding chaperone binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0045901 positive regulation of translational elongation
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5jup, PDBe:5jup, PDBj:5jup
• PDBsum: 5jup
• PubMed: 27159452
• UniProt: P32324|EF2_YEAST Elongation factor 2 (Gene Name=EFT1)