2XI2: HCV-H77 NS5B Apo Polymerase

HCV-H77 NS5B Apo Polymerase. Determined by X-ray diffraction at 1.8 Å resolution. Released 4 Aug 2010.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Hepatitis C virus genotype 1a (isolate H77)
Chains: 3
Atoms: 14,490
Mol. weight: 193.28 kDa
Released: 4 Aug 2010

Explore 2XI2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XI2 contains 124 α-helices and 85 β-strands across 3 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: 42 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	4-6	3	2
α-helix	9-11	3
β-strand	20	1	3
α-helix	21-23	3
α-helix	25-30	6
α-helix	34-36	3
β-strand	37-39	3	3
α-helix	42-44	3
α-helix	45-52	8
β-strand	55	1	1
α-helix	62-75	14
β-strand	79	1	4
α-helix	82-84	3
α-helix	85-90	6
α-helix	96-99	4
α-helix	105-109	5
α-helix	113-128	16
α-helix	133-135	3
β-strand	136-140	5	2
β-strand	144-146	3	3
β-strand	148	1	5
β-strand	153	1	5
α-helix	155-158	4
β-strand	159-162	4	2
α-helix	165-187	23
α-helix	188-190	3
β-strand	191	1	6
α-helix	192-194	3
α-helix	197-210	14
β-strand	214-219	6	6
β-strand	221	1	7
α-helix	224-227	4
α-helix	230-240	11
β-strand	244	1	4
α-helix	247-256	10
α-helix	257-261	5
β-strand	264-267	4	2
β-strand	273-277	5	2
α-helix	287-305	19
β-strand	309-316	8	6
β-strand	319-325	7	6
α-helix	329-345	17
β-strand	350	1	7
α-helix	353-354	2
β-strand	357	1	6
α-helix	360-362	3
β-strand	365	1	8
β-strand	368-374	7	8
β-strand	380-386	7	8
α-helix	389-400	12
β-strand	406	1	9
α-helix	408-414	7
α-helix	419-420	2
α-helix	421-426	6
α-helix	427-435	9
β-strand	443-447	5	9
β-strand	450-454	5	9
α-helix	456-458	3
α-helix	459-467	9
α-helix	469-472	4
β-strand	475	1	8
α-helix	479-492	14
α-helix	494-496	3
α-helix	497-514	18
α-helix	516-520	5
α-helix	521-525	5
α-helix	527-529	3
α-helix	533-536	4
α-helix	540-544	5
β-strand	561	1	9

Chain B: 39 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	10
β-strand	4-6	3	11
α-helix	25-28	4
α-helix	34-36	3
β-strand	37-39	3	12
α-helix	42-44	3
α-helix	45-52	8
β-strand	55	1	10
α-helix	62-75	14
β-strand	79	1	13
α-helix	82-84	3
α-helix	85-90	6
α-helix	97-99	3
α-helix	105-109	5
α-helix	113-128	16
α-helix	133-135	3
β-strand	136-140	5	11
β-strand	144-146	3	12
β-strand	148	1	14
β-strand	153	1	14
α-helix	155-158	4
β-strand	159-162	4	11
α-helix	165-187	23
α-helix	188-190	3
β-strand	191	1	15
α-helix	192-194	3
α-helix	197-209	13
β-strand	214-219	6	15
β-strand	221	1	16
α-helix	224-227	4
α-helix	230-242	13
β-strand	244	1	13
α-helix	247-256	10
α-helix	257-261	5
β-strand	264-267	4	11
β-strand	273-277	5	11
α-helix	287-306	20
β-strand	312-316	5	15
β-strand	319-325	7	15
α-helix	329-345	17
β-strand	350	1	16
α-helix	353-354	2
β-strand	357	1	15
α-helix	360-362	3
β-strand	365	1	17
β-strand	368-374	7	17
β-strand	380-386	7	17
α-helix	389-400	12
α-helix	407-415	9
α-helix	419-420	2
α-helix	421-426	6
α-helix	427-435	9
β-strand	443-447	5	18
β-strand	450-454	5	18
α-helix	456-458	3
α-helix	459-467	9
α-helix	469-472	4
β-strand	475	1	17
α-helix	479-492	14
α-helix	494-496	3
α-helix	497-512	16
α-helix	516-525	10
α-helix	527-529	3
α-helix	537-539	3
α-helix	540-544	5
β-strand	561	1	18

Chain C: 43 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	19
β-strand	4-6	3	20
α-helix	9-11	3
β-strand	20	1	21
α-helix	21-23	3
α-helix	25-30	6
α-helix	34-36	3
β-strand	37-39	3	21
α-helix	42-44	3
α-helix	45-52	8
β-strand	55	1	19
α-helix	62-75	14
β-strand	79	1	22
α-helix	81-84	4
α-helix	85-90	6
α-helix	96-99	4
α-helix	105-109	5
α-helix	113-128	16
α-helix	133-135	3
β-strand	136-140	5	20
β-strand	144-146	3	21
β-strand	148	1	23
β-strand	153	1	23
α-helix	155-158	4
β-strand	159-162	4	20
α-helix	165-187	23
α-helix	188-190	3
β-strand	191	1	24
α-helix	192-194	3
α-helix	197-209	13
β-strand	214-220	7	24
β-strand	221	1	25
α-helix	224-227	4
α-helix	230-240	11
β-strand	244	1	22
α-helix	247-256	10
α-helix	257-261	5
β-strand	264-267	4	20
β-strand	273-277	5	20
α-helix	287-306	20
β-strand	309-316	8	24
β-strand	319-325	7	24
α-helix	329-345	17
β-strand	350	1	25
α-helix	353-354	2
β-strand	357	1	24
α-helix	360-362	3
β-strand	365	1	26
β-strand	368	1	26
β-strand	369-374	6	27
β-strand	380-385	6	27
α-helix	389-400	12
α-helix	407-414	8
α-helix	419-420	2
α-helix	421-425	5
α-helix	426-435	10
β-strand	443-447	5	28
β-strand	450-454	5	28
α-helix	456-458	3
α-helix	459-467	9
α-helix	469-472	4
β-strand	475	1	27
α-helix	479-492	14
α-helix	494-496	3
α-helix	497-514	18
α-helix	516-520	5
α-helix	521-525	5
α-helix	527-529	3
α-helix	533-535	3
α-helix	537-539	3
α-helix	540-542	3
β-strand	561	1	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase	A, B, C	protein	576	Hepatitis C virus genotype 1a (isolate H77)	P27958 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>2XI2_1 RNA-directed RNA polymerase (chains A, B, C)
SMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNLVYSTTSRSACQRQKKVTFDRLQVL
DSHYHDVLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKFGYGAKDVRCHARKAVAHIN
SVWKDLLEDSVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVS
KLPLAVMGSSYGFQYSPGQRVEFLVQAWKSKKTPMGFSYDTRCFDSTVTESDIRTEEAIY
QCCDLDPQARVAIKSLTERLYVGGPLTNSRGENCGYRRCRASGVLTTSCGNTLTCYIKAR
AACRAAGLQDCTMLVCGDDLVVICESAGVQEDAASLRAFTEAMTRYSAPPGDPPQPEYDL
ELITSCSSNVSVAHDGAGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMFAPTLW
ARMILMTHFFSVLIARDQLEQALNCEIYGACYSIEPLDLPPIIQRLHGLSAFSLHSYSPG
EINRVAACLRKLGVPPLRAWRHRARSVRARLLSRGGRAAICGKYLFNWAVRTKLKLTPIA
AAGRLDLSGWFTAGYSGGDIYHSVSHARPRHHHHHH

Primary citation

Further Insights Into the Roles of GTP and the C- Terminus of the Hepatitis C Virus Polymerase in the Initiation of RNA Synthesis. Harrus, D., Ahmed-El-Sayed, N., Simister, P.C. et al. J Biol Chem (2010) 285:32906. DOI 10.1074/JBC.M110.151316 · PubMed

Other PDB entries of the same protein (UniProt P27958 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BZY 1.6 Å, Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423…
5FGB 1.65 Å, Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV)…
6BQJ 1.69 Å, Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl…
2XI3 1.7 Å, HCV-H77 NS5B Polymerase Complexed With GTP
4N0Y 1.75 Å, Structure of the Hepatitis C Envelope Glycoprotein E1 antigenic region 314-324 bound to…
6UYD 1.9 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from…
5FGC 1.9 Å, Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV)…
6BQK 1.97 Å, Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl…
5EOC 1.98 Å, Crystal structure of Fab C2 in complex with a Cyclic variant of Hepatitis C Virus E2…
2O8M 2.0 Å, Crystal structure of the S139A mutant of Hepatitis C Virus NS3/4A protease
4XVJ 2.0 Å, Structure of the hepatitis C virus envelope glycoprotein E2 antigenic 2 region 412-423…
4Z0X 2.0 Å, Structure of Hepatitis C Virus Envelope glycoprotein E2 antigenic region 434-446 bound…

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