4KZX: Rabbit 40S ribosomal subunit

Rabbit 40S ribosomal subunit in complex with eIF1. Determined by X-ray diffraction at 7.81 Å resolution. Released 24 Jul 2013.

Method: X-ray diffraction
Resolution: 7.81 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 35
Atoms: 77,211
Mol. weight: 1238.65 kDa
Released: 24 Jul 2013

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

Secondary structure: helices and β-sheets

4KZX contains 183 α-helices and 254 β-strands across 34 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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	19	1
β-strand	20-21	2	5
β-strand	30-31	2	5
β-strand	36-43	8	6
α-helix	50-56	7
β-strand	57	1	64
β-strand	66-73	8	6
α-helix	75-80	6
α-helix	91-93	3

Chain A: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	5	1	1
α-helix	12-21	10
β-strand	25-26	2	2
α-helix	35-37	3
β-strand	38-42	5	2
β-strand	46-49	4	2
α-helix	51-65	15
α-helix	71-73	3
β-strand	75-78	4	3
α-helix	81-83	3
α-helix	84-93	10
β-strand	97-100	4	3
β-strand	122-124	3	3
α-helix	131-137	7
β-strand	144-146	3	3
β-strand	147-148	2	4
β-strand	161-162	2	4
α-helix	168-184	17
α-helix	199-201	3

Chain b: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	32-35	4	9
β-strand	44-47	4	9
β-strand	49	1	10
β-strand	65	1	11
β-strand	70	1	10
β-strand	72	1	11

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	28-34	7	7
β-strand	43-50	8	7
α-helix	51-52	2
β-strand	53	1	8
β-strand	56	1	8
α-helix	60-63	4
β-strand	66-70	5	7
α-helix	71-75	5
β-strand	83-92	10	7
β-strand	95-104	10	7
α-helix	108-113	6
β-strand	120-128	9	7
β-strand	134-142	9	7
α-helix	155-157	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-201	10
β-strand	208-219	12	7
α-helix	225-231	7

Chain c: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	15
β-strand	27-33	7	15
β-strand	41-46	6	15
β-strand	55-58	4	15

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	50-56	7
α-helix	63-69	7
α-helix	76-82	7
β-strand	84	1	12
β-strand	86	1	12
β-strand	88-93	6	13
β-strand	96-97	2	13
β-strand	108-116	9	13
β-strand	121-129	9	13
α-helix	132-145	14
β-strand	148-149	2	13
β-strand	169-173	5	14
β-strand	176-182	7	14
β-strand	189-190	2	14
α-helix	193-202	10
β-strand	207-212	6	14
α-helix	215-217	3
α-helix	219-234	16
α-helix	238-241	4
α-helix	250-253	4

Chain d: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	30-31	2	19
α-helix	33-35	3
β-strand	38-39	2	19
α-helix	40-50	11
β-strand	53	1	75

Chain D: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-41	8	16
β-strand	46-52	7	16
α-helix	55-59	5
α-helix	65-76	12
β-strand	84-89	6	16
α-helix	90-91	2
α-helix	99-111	13
α-helix	116-129	14
β-strand	133-140	8	17
β-strand	148-155	8	17
α-helix	163-167	5
β-strand	168-176	9	17
β-strand	181-189	9	17
α-helix	192-195	4
β-strand	209-210	2	18
α-helix	211	1

26 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
40S ribosomal protein SA	A	protein	295	Oryctolagus cuniculus	G1TGI6 (AlphaFold model)
40S ribosomal protein S3a	B	protein	264	Oryctolagus cuniculus	G1TN72 (AlphaFold model)
40S ribosomal protein S2	C	protein	278	Oryctolagus cuniculus	G1U2Z9 (AlphaFold model)
40S ribosomal protein S3	D	protein	243	Oryctolagus cuniculus	G1TNM3 (AlphaFold model)
40S ribosomal protein S4X	E	protein	263	Oryctolagus cuniculus	G1TK17
40S ribosomal protein S5	F	protein	204	Oryctolagus cuniculus	G1TFM5
40S ribosomal protein S6	G	protein	249	Oryctolagus cuniculus	G1TM55
40S ribosomal protein S7	H	protein	194	Oryctolagus cuniculus	G1SVB0
40S ribosomal protein S8	I	protein	208	Oryctolagus cuniculus	G1TJW1
40S Ribosomal protein S9	J	protein	194	Oryctolagus cuniculus	B7NZS8
40S ribosomal protein S10	K	protein	165	Oryctolagus cuniculus	G1T168
40S ribosomal protein S11	L	protein	158	Oryctolagus cuniculus	G1TRM4

23 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>4KZX_1 40S ribosomal protein SA (chains A)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS

Sequence of entity 2 (B), FASTA

>4KZX_2 40S ribosomal protein S3a (chains B)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLHLFCVGFTKKCNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 3 (C), FASTA

>4KZX_3 40S ribosomal protein S2 (chains C)
MVDDAGAAGGPGGPGGPGMGGRGGFRGGFGSGIRGCGGKAGDKEWLPVTKLGRLVKDMKI
KSLEEIYLFSLPIKESEIIDFFLGAALKDKVLKIMPVQKQTQAGQRTRFKAFVAIGDYNG
HVGLGMKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVRCKVTGRCGSVLVRL
IPAPRGTGIISAPVPKKLLLMAGIDDCYTSAGGCTATLGNFAKATFDAISKTYSYLTPDL
WKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 4 (D), FASTA

>4KZX_4 40S ribosomal protein S3 (chains D)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 5 (E), FASTA

>4KZX_5 40S ribosomal protein S4X (chains E)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 6 (F), FASTA

>4KZX_6 40S ribosomal protein S5 (chains F)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 7 (G), FASTA

>4KZX_7 40S ribosomal protein S6 (chains G)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 8 (H), FASTA

>4KZX_8 40S ribosomal protein S7 (chains H)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 9 (I), FASTA

>4KZX_9 40S ribosomal protein S8 (chains I)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVGVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 10 (J), FASTA

>4KZX_10 40S Ribosomal protein S9 (chains J)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 11 (K), FASTA

>4KZX_11 40S ribosomal protein S10 (chains K)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Sequence of entity 12 (L), FASTA

>4KZX_12 40S ribosomal protein S11 (chains L)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Primary citation

The initiation of mammalian protein synthesis and mRNA scanning mechanism. Lomakin, I.B., Steitz, T.A. Nature (2013) 500:307-311. DOI 10.1038/nature12355 · PubMed

Other PDB entries of the same protein (UniProt G1TGI6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4KZY 7.01 Å, Rabbit 40S ribosomal subunit in complex with eIF1 and eIF1A.
4KZZ 7.03 Å, Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A

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