4V9F: 50S ribosomal protein L2P

The re-refined crystal structure of the Haloarcula marismortui large ribosomal subunit at 2.4 Angstrom resolution: more complete structure of the L7/L12 and L1 stalk, L5 and LX proteins. Determined by X-ray diffraction at 2.4 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Haloarcula marismortui
Chains: 34
Atoms: 103,831
Mol. weight: 1486.4 kDa
Ligands: CD, MG
Released: 9 Jul 2014

Explore 4V9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V9F contains 229 α-helices and 207 β-strands across 32 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 1: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
β-strand	16-18	3	8
β-strand	25-28	4	8
β-strand	33-34	2	8
α-helix	45-46	2
α-helix	49-51	3

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	5-16	12
α-helix	19-22	4
α-helix	23-28	6

Chain 3: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	17
β-strand	6-11	6	18
β-strand	16-24	9	18
α-helix	25-30	6
α-helix	35-43	9
α-helix	50-53	4
α-helix	63	1
β-strand	64	1	19
α-helix	65	1
β-strand	67-71	5	18
β-strand	77-79	3	18
β-strand	84	1	19
β-strand	89-91	3	17

Chain 4: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	19-26	8
α-helix	27-29	3
α-helix	35-44	10

Chain 5: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-11	10
α-helix	20-26	7
α-helix	27-29	3
α-helix	35-43	9
α-helix	50-54	5

Chain 6: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	26
β-strand	17-23	7	26
α-helix	28-43	16
β-strand	51-55	5	26

Chain A: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	14-16	3
α-helix	20-22	3
α-helix	29-31	3
β-strand	37-48	12	4
β-strand	53-60	8	4
β-strand	65-69	5	4
α-helix	70	1
β-strand	71	1	5
β-strand	75	1	3
β-strand	79-83	5	4
β-strand	93-95	3	4
α-helix	96-98	3
α-helix	100	1
β-strand	104-106	3	4
β-strand	108	1	6
β-strand	118	1	6
β-strand	126-130	5	4
β-strand	136-139	4	4
β-strand	145-148	4	4
β-strand	153-156	4	4
β-strand	159	1	5
α-helix	164-166	3
α-helix	172-179	8
α-helix	191-193	3
α-helix	196-198	3
β-strand	214-215	2	7
α-helix	219-220	2
β-strand	227-228	2	7

Chain B: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	37-38	2	9
β-strand	41-54	14	10
β-strand	66-75	10	10
β-strand	79-90	12	11
β-strand	93-101	9	11
α-helix	109-111	3
α-helix	121-134	14
β-strand	137-145	9	11
α-helix	148-150	3
α-helix	159-160	2
β-strand	161-165	5	11
β-strand	166-167	2	9
α-helix	171-183	13
β-strand	187-188	2	11
α-helix	190-193	4
β-strand	199-205	7	10
α-helix	206-208	3
β-strand	210-212	3	12
α-helix	214-218	5
α-helix	220-223	4
α-helix	225-229	5
β-strand	255-257	3	12
β-strand	261-275	15	10
α-helix	279-280	2
β-strand	284	1	13
β-strand	288	1	13
β-strand	292-298	7	10
β-strand	308-313	6	10
β-strand	327-330	4	10

24 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
23S Ribosomal RNA	0	RNA	2910	Haloarcula marismortui
5S Ribosomal RNA	9	RNA	122	Haloarcula marismortui
50S ribosomal protein L2P	A	protein	240	Haloarcula marismortui	P20276 (AlphaFold model)
50S ribosomal protein L3P	B	protein	338	Haloarcula marismortui	P20279 (AlphaFold model)
50S ribosomal protein L4P	C	protein	246	Haloarcula marismortui	P12735 (AlphaFold model)
50S ribosomal protein L5P	D	protein	177	Haloarcula marismortui	P14124 (AlphaFold model)
50S ribosomal protein L6P	E	protein	178	Haloarcula marismortui	P14135
50S ribosomal protein L7Ae	F	protein	120	Haloarcula marismortui	P12743
50S ribosomal protein L10E	G	protein	255	Haloarcula marismortui	P15825
50S ribosomal protein L10e	H	protein	177	Haloarcula marismortui	P60617
50S ribosomal protein L11P	I	protein	162	Haloarcula marismortui	P14122
50S ribosomal protein L13P	J	protein	145	Haloarcula marismortui	P29198

21 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>4V9F_1 23S Ribosomal RNA (chains 0)
ACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAGCUGCGA
UAAGCUGUGGGGAGCCGCACGGAGGCGAAGAACCACAGAUUUCCGAAUGAGAAUCUCUCU
AACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCGGGAGGAA
CAGAAAACGCAACGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCAAACCGA
AGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUUCACGAAG
UCUCUUGGAAUAGAGCGUGAUACAGGGUGACAACCCCGUACUGAAGACCAGUACGCUGUG
CGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAUCGACUGC
GAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCUGCAAAG
UACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGACAGGGCA
UACAAGGUCCCUUGACGAAUGACCGAGACGCGAGUCUCCAGUAAGACUCACGGGAAGCCG
AUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGUAUGGCAAGUCUAAC
CGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCGAGGGCCG
CCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUACGCAUGG
ACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUACAAUAC
CCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUGGUUCCA
AUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUU
GGUGUGUCCGCCUCCGAGAGGAGUCGGCCCUCCUGUCAAACUCCAAACUUACAGACGCUG
UUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACAACCCAG
AGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUCUCGAGCC
CUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAACAGCUUA
CCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGACCUGUC
CGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGCAGGGGCG
AGAGCUCCUGUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUAGUCGGG
UGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUGAGGGUU
AGCCGGUCCUAAGUCUCACCGCAACUCGACUGAGACGAAAUGGGAAACAGGUUAAUAUUC
CUGUGCCAUCAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCCGGGCAUUCGCCCG
GUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGCGGCAUAG
GGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUGAUGUCCGUACCGAGAACC
GACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUUAGGGAA
UUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGGAGCAGGU
CGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUCCGCAAG
GACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUACAAGAGGA
CGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGUACCUUGC
CGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACGUUGGGC
CCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAAGACCCU
AUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUAGGUAGGA
GACACUACACAGGUACCCGCGCUAGCGGGCCACCGAGUCAACAGUGAAAUACUACCCGUC
GGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGACUGGGGC
GGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGUCAUCUCAGCCGGGACAGAGACC
CGGCGAAGAGUGCAAGAGCAAAAGAUGACUUGACAGUGUUCUUCCCAACGAGGAACGCUG
ACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGAUGACAGA
AAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCGAGUGGCU
UGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGGUGAGGUU
GUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUCGGCUGC
UAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAGGAACUAC
GGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCACGCCAC
ACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGA
GGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACG
UUAAGCCCACGAGCACUAACAGACCAAAGC

Sequence of entity 2 (9), FASTA

>4V9F_2 5S Ribosomal RNA (chains 9)
UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCC
CACCAGCGUUCCAGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCA
CC

Sequence of entity 3 (A), FASTA

>4V9F_3 50S ribosomal protein L2P (chains A)
MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVE
FEDGDRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFA
RASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKM
KARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE

Sequence of entity 4 (B), FASTA

>4V9F_4 50S ribosomal protein L3P (chains B)
MPQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTHVVLVNDEPN
SPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDH
DPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHAL
DIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNL
GPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKG
SVPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG

Sequence of entity 5 (C), FASTA

>4V9F_5 50S ribosomal protein L4P (chains C)
MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAES
FGSGRGQAHVPKQDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATAD
ADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGS
ARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESAL
AEVAER

Sequence of entity 6 (D), FASTA

>4V9F_6 50S ribosomal protein L5P (chains D)
MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVG
EFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEY
DPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE

Sequence of entity 7 (E), FASTA

>4V9F_7 50S ribosomal protein L6P (chains E)
MPRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTM
STIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIH
GDTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKPNRGDA

Sequence of entity 8 (F), FASTA

>4V9F_8 50S ribosomal protein L7Ae (chains F)
MPVYVDFDVPADLEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEI
VMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVTDAGEADADVEDIADKVEELR

Sequence of entity 9 (G), FASTA

>4V9F_9 50S ribosomal protein L10E (chains G)
ERKTETIPEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNT
LLERALDDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIV
IPEGDTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIE
PKEVGLDLRAVFADGVLFEPEELELDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXX

Sequence of entity 10 (H), FASTA

>4V9F_10 50S ribosomal protein L10e (chains H)
MSDKPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQL
RHGSLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAF
GKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVERGEELLIA

Sequence of entity 11 (I), FASTA

>4V9F_11 50S ribosomal protein L11P (chains I)
MAGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFDGTEVPVTVKYDDDG
SFEIEVGVPPTAELIKDEAGFETGSGEPQEDFVADLSVDQVKQIAEQKHPDLLSYDLTNA
AKEVVGTCTSLGVTIEGENPREFKERIDAGEYDDVFAAEAQA

Sequence of entity 12 (J), FASTA

>4V9F_12 50S ribosomal protein L13P (chains J)
MSVAEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKR
VDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTS
LDRLSNIKFVTLGEISETLGANKTW

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	5
MG	Magnesium ion	Mg	138

Water and common crystallization additives (ACY, CL, NA, K) are not listed.

Primary citation

Revisiting the Haloarcula marismortui 50S ribosomal subunit model. Gabdulkhakov, A., Nikonov, S., Garber, M. Acta Crystallogr D Biol Crystallogr (2013) 69:997-1004. DOI 10.1107/S0907444913004745 · PubMed

Other PDB entries of the same protein (UniProt P20276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1VQ8 2.2 Å, The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large…
1VQO 2.2 Å, The structure of CCPMN bound to the large ribosomal subunit haloarcula marismortui
1VQP 2.25 Å, The structure of the transition state analogue "RAP" bound to the large ribosomal…
1VQK 2.3 Å, The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribosomal subunit of…
1VQL 2.3 Å, The structure of the transition state analogue "DCSN" bound to the large ribosomal…
1VQM 2.3 Å, The structure of the transition state analogue "DAN" bound to the large ribosomal…
1FFK 2.4 Å, Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4 Å…
1JJ2 2.4 Å, Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at…
1S72 2.4 Å, Refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 Å…
1VQ9 2.4 Å, The structure of CCA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large…
1VQN 2.4 Å, The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of…
1YHQ 2.4 Å, Crystal Structure Of Azithromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of…

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