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- PDB-6pze: Crystal structure of human NA-45 Fab in complex with neuraminidas... -

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Basic information

Entry
Database: PDB / ID: 6pze
TitleCrystal structure of human NA-45 Fab in complex with neuraminidase Y169aH mutant from A/Shanghai/2/2013 (H7N9)
Components
  • NA-45 FAB HEAVY CHAIN
  • NA-45 FAB LIGHT CHAIN
  • Neuraminidase
KeywordsIMMUNE SYSTEM / antibody / inhibition mechanism
Function / homology
Function and homology information


exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / exo-alpha-(2->3)-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / integral component of membrane / metal ion binding
Sialidase superfamily / Neuraminidase / Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase - #10 / Neuraminidase / 6 Propeller / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
polysac:dmanpa1-2dmanpa1-2dmanpa1-3[dmanpa1-2dmanpa1-3[dmanpa1-6]dmanpa1-6]dmanpb1-4dglcpnacb1-4dglcpnacb1-: / Neuraminidase / Neuraminidase / polysac:dglcpnacb1-4dglcpnacb1-:
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400024C United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4746
Polymers92,2883
Non-polymers2,1863
Water10,629590
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN

L: NA-45 FAB LIGHT CHAIN
H: NA-45 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)377,89424
Polymers369,15012
Non-polymers8,74412
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_456-x-1,-y,z+11
crystal symmetry operation3_456-y-1/2,x+1/2,z+11
crystal symmetry operation4_446y-1/2,-x-1/2,z+11
Buried area40520 Å2
ΔGint14 kcal/mol
Surface area123810 Å2
MethodPISA
2


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint11 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)161.268, 161.268, 87.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-782-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase /


Mass: 44014.000 Da / Num. of mol.: 1 / Mutation: Y169H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shanghai/02/2013(H7N9))
Strain: A/Shanghai/02/2013(H7N9) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: V9NZ28, UniProt: R4NFR6*PLUS, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules LH

#2: Antibody NA-45 FAB LIGHT CHAIN


Mass: 22909.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody NA-45 FAB HEAVY CHAIN


Mass: 25364.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 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]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 591 molecules

#6: Chemical ChemComp-CA / CALCIUM ION / Calcium


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


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, pH 7.0 and 10% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→45.8 Å / Num. obs: 51133 / % possible obs: 98.3 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rsym value: 0.12 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.35 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3164 / CC1/2: 0.962 / Rpim(I) all: 0.26 / Rsym value: 0.62 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L14, 5T93, 5BV7
Resolution: 2.3→45.786 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.85
RfactorNum. reflection% reflection
Rfree0.1973 2564 5.02 %
Rwork0.1559 --
Obs0.158 51085 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 145 590 6995
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076596
X-RAY DIFFRACTIONf_angle_d0.9449037
X-RAY DIFFRACTIONf_dihedral_angle_d5.6643894
X-RAY DIFFRACTIONf_chiral_restr0.0551031
X-RAY DIFFRACTIONf_plane_restr0.0061132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2.2944-2.33850.25111380.18842631X-RAY DIFFRACTION98
2.3385-2.38620.26421310.18222677X-RAY DIFFRACTION98
2.3862-2.43810.25061550.18182672X-RAY DIFFRACTION99
2.4381-2.49480.22891380.17872626X-RAY DIFFRACTION97
2.4948-2.55720.23621230.17352566X-RAY DIFFRACTION95
2.5572-2.62640.21961430.16822697X-RAY DIFFRACTION99
2.6264-2.70360.20861330.16822688X-RAY DIFFRACTION99
2.7036-2.79090.18771420.15352686X-RAY DIFFRACTION99
2.7909-2.89060.22421370.1572712X-RAY DIFFRACTION99
2.8906-3.00630.20681590.15842698X-RAY DIFFRACTION99
3.0063-3.14310.20441300.16122707X-RAY DIFFRACTION99
3.1431-3.30880.20391230.16012591X-RAY DIFFRACTION94
3.3088-3.5160.17811640.15882716X-RAY DIFFRACTION99
3.516-3.78740.22781300.16972744X-RAY DIFFRACTION99
3.7874-4.16830.16261560.14112759X-RAY DIFFRACTION100
4.1683-4.77090.16311420.11712707X-RAY DIFFRACTION97
4.7709-6.00870.16541680.12992745X-RAY DIFFRACTION98
6.0087-45.79490.19791520.16842899X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.55390.3897-0.22150.4612-0.08160.49760.0378-0.02730.04470.01320.0270.0488-0.00870.0018-0.07470.1630.0208-0.01220.12930.00460.1547-66.197-10.073137.5891
20.3422-0.079-0.25380.82430.06691.26580.0007-0.0038-0.04120.04740.0089-0.02680.0631-0.0677-0.04940.15070.0276-0.02710.1948-0.0260.1464-51.3051-5.21743.4068
30.7936-0.21720.07620.90970.39861.1739-0.0237-0.1273-0.09570.07180.0371-0.09790.05290.1086-0.03660.15240.0395-0.06380.20050.01760.1967-47.0605-17.903846.2027
40.81390.3504-0.05810.6513-0.08370.30340.0307-0.0197-0.10650.01270.0136-0.07590.07120.0869-0.04150.14050.0287-0.02640.149-0.01630.1334-58.2613-21.929234.057
50.85890.03140.3891.2182-0.94763.5533-0.07290.2843-0.2598-0.28950.2370.21190.2068-0.4054-0.1240.3379-0.0089-0.00520.4761-0.05910.2189-47.5155-20.1779-3.6987
62.12740.30430.42621.4840.43163.51830.01530.41940.1792-0.15120.06260.04810.0734-0.0334-0.06110.1743-0.00860.00610.27530.01780.2121-48.754-12.93314.8695
70.4822-0.1397-0.6260.30610.18220.8072-0.25790.04440.20350.008-0.003-0.02780.21550.14190.26220.335-0.0193-0.0980.52210.00570.2536-38.1283-11.7565-17.9329
83.3570.97090.74632.92080.32852.3837-0.21950.47440.0347-0.64170.11-0.2805-0.56670.37010.08550.3927-0.12380.02450.5491-0.0280.3572-20.5651-8.4499-25.3875
90.85980.3579-1.32722.25810.21812.31970.12860.06510.4354-0.03750.0576-0.1877-0.10840.4377-0.18550.2309-0.04380.06920.3099-0.01630.3275-25.11420.65518.4749
101.81731.25710.3541.5909-0.7272.26350.1020.20460.2319-0.02260.09070.0185-0.17520.0057-0.19020.18030.02040.0420.2712-0.06750.2907-36.1313-1.434512.7898
113.44240.1655-0.31143.26180.34923.20930.1637-0.4616-0.10240.16540.0191-0.2386-0.13950.2764-0.15340.2023-0.02440.0060.2583-0.0270.2066-33.9043-5.683722.2792
122.1551-1.1353-0.52510.94370.07571.41650.1007-0.09120.25460.11220.0166-0.2833-0.10520.1449-0.14360.2023-0.04780.0250.2979-0.0490.2663-28.11380.065415.8282
132.210.3522-1.89620.3517-0.27381.65210.21120.22940.26580.11470.18470.0231-0.0691-0.1476-0.30580.19170.03470.01330.2303-0.01040.2338-42.8034-6.264217.3429
143.26120.5717-3.65461.0837-0.60684.1146-0.09580.0520.4339-0.08180.23810.0293-0.0091-0.1255-0.16330.18350.00280.00910.2325-0.01210.2527-39.3763-2.79987.9702
152.51991.10840.10351.63160.36433.7552-0.30850.23420.5892-0.4358-0.04070.3482-0.7663-0.07050.33180.43780.0021-0.07940.33540.00570.4377-21.10411.486-12.7435
160.1645-0.0091-0.002-0.0004-0.0018-0.0010.10011.03560.9809-0.899-0.08760.4131-0.6745-0.0973-0.12911.26680.1426-0.32350.65090.3431.0297-27.188111.1918-25.5233
172.2013-0.78390.89631.1566-0.51841.7082-0.46430.12041.1428-0.6886-0.0360.4558-1.17-0.04940.40350.9056-0.0387-0.20110.37490.05060.8755-19.182910.3189-12.2936
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 82:190 )A82 - 190
2X-RAY DIFFRACTION2( CHAIN A AND RESID 191:246 )A191 - 246
3X-RAY DIFFRACTION3( CHAIN A AND RESID 247:318 )A247 - 318
4X-RAY DIFFRACTION4( CHAIN A AND RESID 319:468 )A319 - 468
5X-RAY DIFFRACTION5( CHAIN L AND RESID 2:18 )L2 - 18
6X-RAY DIFFRACTION6( CHAIN L AND RESID 19:98 )L19 - 98
7X-RAY DIFFRACTION7( CHAIN L AND RESID 99:118 )L99 - 118
8X-RAY DIFFRACTION8( CHAIN L AND RESID 119:208 )L119 - 208
9X-RAY DIFFRACTION9( CHAIN H AND RESID 2:17 )H2 - 17
10X-RAY DIFFRACTION10( CHAIN H AND RESID 18:51 )H18 - 51
11X-RAY DIFFRACTION11( CHAIN H AND RESID 52:66 )H52 - 66
12X-RAY DIFFRACTION12( CHAIN H AND RESID 67:87 )H67 - 87
13X-RAY DIFFRACTION13( CHAIN H AND RESID 88:100 )H88 - 100
14X-RAY DIFFRACTION14( CHAIN H AND RESID 101:109 )H101 - 109
15X-RAY DIFFRACTION15( CHAIN H AND RESID 110:177 )H110 - 177
16X-RAY DIFFRACTION16( CHAIN H AND RESID 178:194 )H178 - 194
17X-RAY DIFFRACTION17( CHAIN H AND RESID 195:213 )H195 - 213

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