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- PDB-3opz: Crystal structure of trans-sialidase in complex with the Fab frag... -

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Basic information

Entry
Database: PDB / ID: 3opz
TitleCrystal structure of trans-sialidase in complex with the Fab fragment of a neutralizing monoclonal IgG antibody
Components
  • Trans-sialidase
  • heavy chain of the Fab fragment of immunoglobulin G
  • light chain of the Fab fragment of immunoglobulin G
Keywordshydrolase/immune system / six-bladed beta-propeller neuraminidase immunoglobulin domain / viral protein-immune system complex / hydrolase-immune system complex
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / membrane / cytoplasm
Similarity search - Function
: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase ...: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Trans-sialidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsLarrieux, N. / Muia, R. / Campetella, O. / Buschiazzo, A.
CitationJournal: Plos Pathog. / Year: 2012
Title: Trypanosoma cruzi trans-sialidase in complex with a neutralizing antibody: structure/function studies towards the rational design of inhibitors.
Authors: Buschiazzo, A. / Muia, R. / Larrieux, N. / Pitcovsky, T. / Mucci, J. / Campetella, O.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq ...database_2 / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-sialidase
B: Trans-sialidase
C: Trans-sialidase
H: heavy chain of the Fab fragment of immunoglobulin G
I: heavy chain of the Fab fragment of immunoglobulin G
J: heavy chain of the Fab fragment of immunoglobulin G
L: light chain of the Fab fragment of immunoglobulin G
M: light chain of the Fab fragment of immunoglobulin G
N: light chain of the Fab fragment of immunoglobulin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,12412
Polymers355,9259
Non-polymers1993
Water75742
1
A: Trans-sialidase
H: heavy chain of the Fab fragment of immunoglobulin G
L: light chain of the Fab fragment of immunoglobulin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7535
Polymers118,6423
Non-polymers1112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trans-sialidase
I: heavy chain of the Fab fragment of immunoglobulin G
M: light chain of the Fab fragment of immunoglobulin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7304
Polymers118,6423
Non-polymers881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Trans-sialidase
J: heavy chain of the Fab fragment of immunoglobulin G
N: light chain of the Fab fragment of immunoglobulin G


Theoretical massNumber of molelcules
Total (without water)118,6423
Polymers118,6423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.140, 178.140, 140.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B C
12L M N
13H I J
21A B C
22L M N
23H I J
31A B C
32L M N
33H I J

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUMETMETAA1 - 63315 - 647
21LEULEUMETMETBB1 - 63315 - 647
31LEULEUMETMETCC1 - 63315 - 647
12VALVALGLUGLULG2 - 2122 - 212
22VALVALGLUGLUMH2 - 2122 - 212
32VALVALGLUGLUNI2 - 2122 - 212
13VALVALTHRTHRHD2 - 2221 - 221
23VALVALTHRTHRIE2 - 2221 - 221
33VALVALTHRTHRJF2 - 2221 - 221

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is a heterotrimer, with three trimers in the ASU (chains A-H-L, B-I-M and C-J-N). Each heterotrimers corresponds to a stable binary complex between trans-sialidase (e.g. chain A) and a Fab IgG fragment, itself a heterodimer (chains H and L).

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Trans-sialidase


Mass: 71389.258 Da / Num. of mol.: 3
Mutation: N59F,S263T,R477H,V485L,S496K,V497G,E521K,E559V,D594G,I598D,H600R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): Top10f / References: UniProt: Q26966, exo-alpha-sialidase

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Antibody , 2 types, 6 molecules HIJLMN

#2: Antibody heavy chain of the Fab fragment of immunoglobulin G


Mass: 23869.732 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: monoclonal antibody was obtained from hybridomas (after fusion of mice splenocytes with Sp2/0 cells), and the Fab fragment obtained by standard papain digestion
Source: (natural) Mus musculus (house mouse) / Strain: C3H/HeJ
#3: Antibody light chain of the Fab fragment of immunoglobulin G


Mass: 23382.764 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: monoclonal antibody was obtained from hybridomas (after fusion of mice splenocytes with Sp2/0 cells), and the Fab fragment obtained by standard papain digestion
Source: (natural) Mus musculus (house mouse) / Strain: C3H/HeJ

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Non-polymers , 3 types, 45 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsAUTHORS STATE THAT UNIPROT ENTRY Q26966 HAS FOUR SEQUENCE ERRORS. THESE DISCREPANCIES HAVE BEEN ...AUTHORS STATE THAT UNIPROT ENTRY Q26966 HAS FOUR SEQUENCE ERRORS. THESE DISCREPANCIES HAVE BEEN REPEATEDLY INDICATED IN ALL PROVIOUS XRAY STRUCTURES RELATED TO TRYPANOSOMA CRUZI TRANS-SIALIDASE. THESE ERRORS CONCERN RESIDUES 262 (INDEED A THR), 476 (A HIS), 484 (A LEU) AND 558 (A VAL). HENCE, THESE DISCREPANCIES IN CHAINS A, B AND C, ARE NOT THE RESULT OF PROTEIN ENGINEERING.

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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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bicina, 10 % PEG 20000, 4% 1,4-dioxano, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2009 / Details: Varimax HF multilayer mirrors
RadiationMonochromator: multilayer mirrors (Varimax HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→154.273 Å / Num. all: 68611 / Num. obs: 68611 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.19 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.4-3.583.50.5161.535581100260.516100
3.58-3.83.60.3632.13394695060.363100
3.8-4.063.60.3022.53219489700.302100
4.06-4.393.60.2053.72975982830.205100
4.39-4.813.60.1485.12749976280.148100
4.81-5.383.60.145.42504569190.14100
5.38-6.213.60.15252201160860.152100
6.21-7.63.60.1295.81865351290.129100
7.6-10.753.60.06610.31456639990.066100
10.75-29.793.60.04713.1751320650.04795.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.39 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.4 Å29.79 Å
Translation3.4 Å29.79 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→29.79 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.1811 / WRfactor Rwork: 0.1456 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8948 / SU B: 44.979 / SU ML: 0.316 / SU R Cruickshank DPI: 0.3886 / SU Rfree: 0.4221 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.422 / Stereochemistry target values: Engh & Huber / Details: U VALUES : WITH TLS COMPONENT INCLUDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 1014 1.5 %RANDOM
Rwork0.164 ---
all0.1647 68587 --
obs0.1647 68587 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 203.88 Å2 / Biso mean: 59.3104 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24414 0 13 42 24469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02225030
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.94234035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68253158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1323.8061022
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.703154033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.63315123
X-RAY DIFFRACTIONr_chiral_restr0.0990.23790
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118855
LS refinement shellResolution: 3.4→3.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 70 -
Rwork0.251 4974 -
all-5044 -
obs--100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16040.38-0.66460.9099-0.56341.67990.1003-0.19390.1630.0378-0.0331-0.05760.00790.1691-0.06710.18130.01790.0080.0865-0.08140.09214.60814.3470.256
21.03070.14510.18871.48940.62951.5560.2031-0.2889-0.1434-0.0199-0.03730.13590.18-0.1383-0.16590.2164-0.1047-0.14810.18040.1090.133386.58431.366-35.124
31.7513-0.1354-0.92790.6920.17881.5382-0.0390.26140.1718-0.0822-0.03080.0627-0.0957-0.24820.06980.23260.0079-0.09470.18090.05470.335671.887-41.2163.497
41.2981.53840.79323.02712.71134.76190.02920.0584-0.09340.0669-0.14120.26640.1526-0.21570.1120.10.08120.01340.2218-0.0820.224835.4840.296-33.37
56.536-1.8451.92883.27980.72492.02840.0036-0.343-0.64290.05780.04750.16470.37460.0421-0.05110.16290.07630.020.3385-0.0060.188654.136-28.38-47.336
64.3921-3.0150.28285.50841.5354.07280.1355-0.12280.36760.16460.0506-0.3562-0.06830.8126-0.18610.15170.03060.02540.4012-0.13720.190754.1525.417-23.421
73.9994-0.84670.72255.08811.84629.482-0.15250.20840.2248-0.36710.1889-0.16520.0207-0.0391-0.03640.06770.04960.02450.3327-0.0080.334764.591-16.691-48.593
82.9883-0.74961.71384.2698-2.15592.78140.38990.0796-0.1128-0.1145-0.1280.13640.1992-0.2423-0.26180.1861-0.0725-0.12720.17750.1070.192361.77829.005-68.803
96.3631.0126-0.44433.3658-0.71112.11270.3455-0.12270.2179-0.0265-0.23160.56650.0175-0.6408-0.11390.2587-0.0647-0.06450.4510.01120.265829.0837.911-83.953
107.69620.88313.07191.38-1.0053.03380.6777-0.6073-1.01420.06560.07570.17140.7679-0.7279-0.75330.8007-0.5089-0.2980.51880.31010.517250.49513.077-59.239
116.53141.519-1.57353.1988-2.11959.23080.16110.26-0.6911-0.5476-0.0353-0.01510.5758-0.5439-0.12570.4412-0.1784-0.14870.3968-0.0540.520730.46722.365-85.229
122.4421-2.13150.10274.3015-2.01832.4072-0.1112-0.1946-0.19180.282-0.0596-0.06980.088-0.26840.17080.1205-0.1056-0.05520.3403-0.06850.451154.497-59.7636.593
130.9531-1.27090.47571.8491-0.20782.61150.1953-0.2587-0.7034-0.00890.39910.6940.919-0.8044-0.59440.6518-0.3419-0.18980.86310.20141.300242.521-92.06650.477
143.71661.56760.02854.3-2.40153.95230.0804-0.02020.05670.0356-0.03830.5052-0.1999-0.7778-0.04210.1665-0.0099-0.02710.5624-0.03290.536335.184-59.09126.686
153.3926-0.86395.08452.2553-0.99769.70140.0903-0.957-0.76190.32090.69340.85610.4843-0.9796-0.78370.469-0.23610.14621.38150.31961.288730.288-82.20551.674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 633
2X-RAY DIFFRACTION2B1 - 633
3X-RAY DIFFRACTION3C1 - 633
4X-RAY DIFFRACTION4L1 - 106
5X-RAY DIFFRACTION5L107 - 212
6X-RAY DIFFRACTION6H2 - 118
7X-RAY DIFFRACTION7H119 - 222
8X-RAY DIFFRACTION8M1 - 106
9X-RAY DIFFRACTION9M107 - 212
10X-RAY DIFFRACTION10I4 - 118
11X-RAY DIFFRACTION11I119 - 219
12X-RAY DIFFRACTION12N1 - 106
13X-RAY DIFFRACTION13N107 - 212
14X-RAY DIFFRACTION14J2 - 118
15X-RAY DIFFRACTION15J119 - 219

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