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- PDB-1nca: REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE... -

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Entry
Database: PDB / ID: 1nca
TitleREFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX
Components
  • (IGG2A-KAPPA NC41 FAB ...) x 2
  • INFLUENZA A SUBTYPE N9 NEURAMINIDASE
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / viral budding from plasma membrane / response to bacterium / positive regulation of immune response / antibacterial humoral response / carbohydrate metabolic process / host cell plasma membrane / virion membrane / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig gamma-2A chain C region, membrane-bound form / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTulip, W.R. / Varghese, J.N. / Colman, P.M.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex.
Authors: Tulip, W.R. / Varghese, J.N. / Laver, W.G. / Webster, R.G. / Colman, P.M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal Structures of Two Mutant Neuraminidase-Antibody Complexes with Amino Acid Substitutions in the Interface
Authors: Tulip, W.R. / Varghese, J.N. / Webster, R.G. / Laver, W.G. / Colman, P.M.
#2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1989
Title: Crystal Structures of Neuraminidase-Antibody Complexes
Authors: Tulip, W.R. / Varghese, J.N. / Webster, R.G. / Air, G.M. / Laver, W.G. / Colman, P.M.
#3: Journal: Nature / Year: 1987
Title: Three-Dimensional Structure of a Complex of Antibody with Influenza Virus Neuraminidase
Authors: Colman, P.M. / Laver, W.G. / Varghese, J.N. / Baker, A.T. / Tulloch, P.A. / Air, G.M. / Webster, R.G.
History
DepositionJan 21, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7417
Polymers91,1863
Non-polymers1,5554
Water1,29772
1
N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,96428
Polymers364,74212
Non-polymers6,22216
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
MethodPQS
2
N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,03952
Polymers634,59520
Non-polymers12,44432
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
crystal symmetry operation5_547-x+1/2,y-1/2,-z+21
crystal symmetry operation6_557x+1/2,-y+1/2,-z+21
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_657-y+1,-x,-z+21
Buried area42910 Å2
ΔGint-93 kcal/mol
Surface area120040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.000, 167.000, 124.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Atom site foot note1: RESIDUES PRO N 326, PRO N 431, PRO L 8, PRO L 95, PRO L 141, PRO H 149, PRO H 151 AND PRO H 200 ARE CIS PROLINES.
2: THE COORDINATES OF THE CALCIUM ATOM ARE NOT WELL DETERMINED. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9).
DetailsTHE COORDINATES OF THE CARBOHYDRATE IN THE EPITOPE CAN BE GENERATED FORM THE COORDINATES OF RESIDUES C 200A-C 200F BY APPLYING THE FOLLOWING TRANSFORMATION: 0.0 1.0 0.0 83.5 -1.0 0.0 0.0 83.5 0.0 0.0 1.0 0.0

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Components

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Protein , 1 types, 1 molecules N

#1: Protein INFLUENZA A SUBTYPE N9 NEURAMINIDASE


Mass: 43836.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: (A/tern/Australia/G70C/1975(H11N9)) / References: UniProt: P03472, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules LH

#2: Antibody IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)


Mass: 23722.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: EMBL: Y11589
#3: Antibody IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)


Mass: 23626.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865

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Sugars , 2 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 73 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.04 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: potassium phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å
Details: THE COORDINATES OF THE CALCIUM ATOM ARE NOT WELL DETERMINED. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9).
RfactorNum. reflection
Rwork0.191 -
obs0.191 31846
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 101 72 6577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 31846 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.6
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_deg1.7

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