6YBS: PDB entry 6YBS

Name: PDB 6YBS: Structure of a human 48S translational initiation complex - head
Published: 2020-09-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of a human 48S translational initiation complex - head. Determined by electron microscopy at 3.1 Å resolution. Released 16 Sept 2020.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 18
Atoms: 28,732
Mol. weight: 964.56 kDa
Ligands: ZN, MG
Released: 16 Sept 2020

Explore 6YBS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YBS contains 95 α-helices and 130 β-strands across 17 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 a: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-24	5	21
α-helix	36-38	3
α-helix	42-53	12
β-strand	58-62	5	21
β-strand	66-71	6	21
α-helix	73-82	10

Chain b: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	25
β-strand	20	1	25
α-helix	22-27	6
α-helix	30-34	5
α-helix	39-46	8
α-helix	48-49	2
α-helix	51-64	14
α-helix	68	1
α-helix	72-75	4
β-strand	76-78	3	26
β-strand	84	1	27
β-strand	93-97	5	26
β-strand	102-106	5	26
α-helix	107-108	2
α-helix	109-111	3
β-strand	115	1	27
α-helix	117-119	3

Chain c: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	8
β-strand	18-22	5	9
β-strand	32-35	4	9
β-strand	40-44	5	9
β-strand	54-59	6	9
β-strand	66-71	6	10
β-strand	77-82	6	10
β-strand	87-91	5	10
β-strand	96-101	6	10
β-strand	108-113	6	11
β-strand	119-124	6	11
β-strand	129-133	5	11
β-strand	138-142	5	11
β-strand	151-155	5	12
β-strand	164-169	6	12
β-strand	174-178	5	12
β-strand	183-188	6	12
β-strand	195-200	6	13
β-strand	206-211	6	13
β-strand	215-220	6	13
β-strand	226-231	6	13
β-strand	236-241	6	14
β-strand	247-252	6	14
β-strand	255-260	6	14
β-strand	266-270	5	14
α-helix	272-274	3
α-helix	282-286	5
β-strand	288-291	4	8
β-strand	297-301	5	8
β-strand	307-312	6	8

Chain d: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	11-24	14
α-helix	34-36	3
β-strand	40	1	29
α-helix	52-65	14
β-strand	70	1	30
α-helix	72-78	7
β-strand	81-85	5	31
β-strand	88-93	6	31
β-strand	95	1	29
α-helix	97-109	13
β-strand	113-115	3	30
β-strand	121-123	3	30
α-helix	125-142	18

Chain e: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	32
α-helix	52-61	10
α-helix	62-64	3
β-strand	68	1	33
α-helix	73-76	4
β-strand	79	1	32
α-helix	81-94	14
β-strand	99-102	4	33
β-strand	107-109	3	33

Chain f: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	34
β-strand	20-21	2	34
β-strand	25	1	35
α-helix	26-29	4
α-helix	30-32	3
α-helix	38-47	10
β-strand	55	1	35
α-helix	56-58	3
α-helix	61-72	12
α-helix	75-77	3
α-helix	81-83	3
β-strand	86	1	36
β-strand	96	1	36
α-helix	102-116	15
α-helix	120-127	8

Chain h: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	20-26	7	17
α-helix	29-45	17
β-strand	51-55	5	17
α-helix	56-58	3
β-strand	59-66	8	18
β-strand	77-84	8	18
β-strand	85-91	7	17
α-helix	95-101	7
β-strand	110-116	7	17

Chain i: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	24
α-helix	33-35	3
β-strand	38-39	2	24
α-helix	40-50	11
β-strand	53	1	18

9 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
Eukaryotic translation initiation factor 3 subunit D	x	protein	548	Homo sapiens	O15371 (AlphaFold model)
Receptor of activated protein C kinase 1	c	protein	317	Homo sapiens	P63244 (AlphaFold model)
40S ribosomal protein S28	n	protein	69	Homo sapiens	P62857 (AlphaFold model)
40S ribosomal protein S17	X	protein	135	Homo sapiens	P08708 (AlphaFold model)
40S ribosomal protein S20	h	protein	119	Homo sapiens	P60866
Eukaryotic translation initiation factor 3 subunit G	o	protein	320	Homo sapiens	O75821
40S ribosomal protein S10	a	protein	165	Homo sapiens	P46783
40S ribosomal protein S12	m	protein	132	Homo sapiens	P25398
40S ribosomal protein S29	i	protein	56	Homo sapiens	P62273
40S ribosomal protein S15	b	protein	145	Homo sapiens	P62841
40S ribosomal protein S3	Z	protein	243	Homo sapiens	P23396
40S ribosomal protein S19	d	protein	145	Homo sapiens	P39019

6 more molecules are not listed.

Sequence of entity 1 (x), FASTA

>6YBS_1 Eukaryotic translation initiation factor 3 subunit D (chains x)
MAKFMTPVIQDNPSGWGPCAVPEQFRDMPYQPFSKGDRLGKVADWTGATYQDKRYTNKYS
SQFGGGSQYAYFHEEDESSFQLVDTARTQKTAYQRNRMRFAQRNLRRDKDRRNMLQFNLQ
ILPKSAKQKERERIRLQKKFQKQFGVRQKWDQKSQKPRDSSVEVRSDWEVKEEMDFPQLM
KMRYLEVSEPQDIECCGALEYYDKAFDRITTRSEKPLRSIKRIFHTVTTTDDPVIRKLAK
TQGNVFATDAILATLMSCTRSVYSWDIVVQRVGSKLFFDKRDNSDFDLLTVSETANEPPQ
DEGNSFNSPRNLAMEATYINHNFSQQCLRMGKERYNFPNPNPFVEDDMDKNEIASVAYRY
RRWKLGDDIDLIVRCEHDGVMTGANGEVSFINIKTLNEWDSRHCNGVDWRQKLDSQRGAV
IATELKNNSYKLARWTCCALLAGSEYLKLGYVSRYHVKDSSRHVILGTQQFKPNEFASQI
NLSVENAWGILRCVIDICMKLEEGKYLILKDPNKQVIRVYSLPDGTFSSDEDEEEEEEEE
EEEEEEET

Sequence of entity 2 (c), FASTA

>6YBS_2 Receptor of activated protein C kinase 1 (chains c)
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALR
GHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQI
VSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLA
NCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALC
FSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFA
GYTDNLVRVWQVTIGTR

Sequence of entity 3 (n), FASTA

>6YBS_3 40S ribosomal protein S28 (chains n)
MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLE
SEREARRLR

Sequence of entity 4 (X), FASTA

>6YBS_4 40S ribosomal protein S17 (chains X)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV

Sequence of entity 5 (h), FASTA

>6YBS_5 40S ribosomal protein S20 (chains h)
MAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKT
LRITTRKTPCGEGSKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA

Sequence of entity 6 (o), FASTA

>6YBS_6 Eukaryotic translation initiation factor 3 subunit G (chains o)
MPTGDFDSKPSWADQVEEEGEDDKCVTSELLKGIPLATGDTSPEPELLPGAPLPPPKEVI
NGNIKTVTEYKIDEDGKKFKIVRTFRIETRKASKAVARRKNWKKFGNSEFDPPGPNVATT
TVSDDVSMTFITSKEDLNCQEEEDPMNKLKGQKIVSCRICKGDHWTTRCPYKDTLGPMQK
ELAEQLGLSTGEKEKLPGELEPVQATQNKTGKYVPPSLRDGASRRGESMQPNRRADDNAT
IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV
SGFGYDHLILNVEWAKPSTN

Sequence of entity 7 (a), FASTA

>6YBS_7 40S ribosomal protein S10 (chains a)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Sequence of entity 8 (m), FASTA

>6YBS_8 40S ribosomal protein S12 (chains m)
MAEEGIAAGGVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPM
YVKLVEALCAEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQA
KDVIEEYFKCKK

Sequence of entity 9 (i), FASTA

>6YBS_9 40S ribosomal protein S29 (chains i)
MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 10 (b), FASTA

>6YBS_10 40S ribosomal protein S15 (chains b)
MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRL
RKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFS
ITYKPVKHGRPGIGATHSSRFIPLK

Sequence of entity 11 (Z), FASTA

>6YBS_11 40S ribosomal protein S3 (chains Z)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 12 (d), FASTA

>6YBS_12 40S ribosomal protein S19 (chains d)
MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAAST
ARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGG
RKLTPQGQRDLDRIAGQVAAANKKH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	29

Primary citation

Structure of a human 48Stranslational initiation complex. Brito Querido, J., Sokabe, M., Kraatz, S. et al. Science (2020) 369:1220-1227. DOI 10.1126/science.aba4904 · PubMed

Other PDB entries of the same protein (UniProt O15371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
6ZON 3.0 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
9KZU 3.0 Å, Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome…
8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
9KN5 3.2 Å, Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3
9KRP 3.2 Å, Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3
6YBD 3.3 Å, Structure of a human 48S translational initiation complex - eIF3

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