Structure of PDB 6vmi Chain v

Receptor sequence

>6vmiv (length=712) Species: 9606 (Homo sapiens)

VIPNEKIRNIGISAHIDSGKTTLTERVLYYTGRIAKMHEVKGKDGVGAVM
DSMELERQRGITIQSAATYTMWKDVNINIIDTPGHVDFTIEVERALRVLD
GAVLVLCAVGGVQCQTMTVNRQMKRYNVPFLTFINKLDRMGSNPARALQQ
MRSKLNHNAAFMQIPMGLEGNFKGIVDLIEERAIYFDGDFGQIVRYGEIP
AELRAAATDHRQELIECVANSDEQLGEMFLEEKIPSISDLKLAIRRATLK
RSFTPVFLGSALKNKGVQPLLDAVLEYLPNPSEVQNYAILNKEDDSKEKT
KILMNSSRDNSHPFVGLAFKLEVGRFGQLTYVRSYQGELKKGDTIYNTRT
RKKVRLQRLARMHADMMEDVEEVYAGDICALFGIDCASGDTFTDKANSGL
SMESIHVPDPVISIAMKPSNKNDLEKFSKGIGRFTREDPTFKVYFDTENK
ETVISGMGELHLEIYAQRLEREYGCPCITGKPKVAFRETITAPVPFDFTH
KKQSGGAGQYGKVIGVLEPLDPEDYTKLEFSDETFGSNIPKQFVPAVEKG
FLDACEKGPLSGHKLSGLRFVLQDGAHHMVDSNEISFIRAGEGALKQALA
NATLCILEPIMAVEVVAPNEFQGQVIAGINRRHGVITGQDGVEDYFTLYA
DVPLNDMFGYSTELRSCTEGKGEYTMEYSRYQPCLPSTQEDVINKYLEAT
GQLPVKKGKAKN

3D structure

• PDB: 6vmi Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation.
• Chain: v
• Resolution: 2.96 Å

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	v	R364 F365 K380 R390 F421 G544 A546 N577 I624	R325 F326 K341 R351 F382 G505 A507 N538 I585
BS02	rna	v	H54 I55 K80 H124 V125 Q152 C153 R178 K541 S543 R628 E631 K635 I665 A666 R670 I675 T676 Q678 T701 R704 S705 E708	H15 I16 K41 H85 V86 Q113 C114 R139 K502 S504 R589 E592 K596 I626 A627 R631 I636 T637 Q639 T662 R665 S666 E669
BS03	rna	v	K540 Q542 G545 Y549 M618 V619	K501 Q503 G506 Y510 M579 V580
BS04	MG	v	K59 T60 T101	K20 T21 T62

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0070125 mitochondrial translational elongation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix

External links

• PDB: RCSB:6vmi, PDBe:6vmi, PDBj:6vmi
• PDBsum: 6vmi
• PubMed: 32737313
• UniProt: Q96RP9|EFGM_HUMAN Elongation factor G, mitochondrial (Gene Name=GFM1)