3j2v

Electron Microscopy
3.5Å resolution

CryoEM structure of HBV core

Released:
Source organism: Hepatitis B virus
Related structures: EMD-2278

Function and Biology Details

Reactions catalysed:
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
GTP = 3',5'-cyclic GMP + diphosphate
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
ATP + AMP = 2 ADP
4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH
An alpha-L-fucoside + H(2)O = L-fucose + an alcohol
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
Beta-D-ribopyranose = beta-D-ribofuranose
(R)-10-hydroxystearate = oleate + H(2)O
GTP + alpha-D-mannose 1-phosphate = diphosphate + GDP-mannose
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
Release of N-terminal proline from a peptide.
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
Geranyl diphosphate = alpha-terpinene + diphosphate
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
Geranyl diphosphate = gamma-terpinene + diphosphate
ATP + a protein = ADP + a phosphoprotein
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
RX + glutathione = HX + R-S-glutathione
(S)-ureidoglycolate = glyoxylate + urea
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
NTP + H(2)O = NDP + phosphate
Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Chorismate = prephenate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
Choline = trimethylamine + acetaldehyde
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
ATP + H(2)O = ADP + phosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
Isocitrate = succinate + glyoxylate
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
(R)-mandelonitrile = cyanide + benzaldehyde
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
Biochemical function:
Cellular component:

Structure analysis Details

Assemblies composition:
homo 240-mer (preferred)
homo tetramer
homo icosamer
homo 24-mer
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Capsid protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 185 amino acids
Theoretical weight: 21.4 KDa
Source organism: Hepatitis B virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P03149 (Residues: 1-185; Coverage: 100%)
Gene name: C
Sequence domains: Hepatitis core antigen
Structure domains: Viral capsid, core domain supefamily, Hepatitis B virus

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-2278
Expression system: Escherichia coli