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- PDB-3qnz: Orthorhombic form of IgG1 Fab fragment (in complex with antigenic... -

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Basic information

Entry
Database: PDB / ID: 3qnz
TitleOrthorhombic form of IgG1 Fab fragment (in complex with antigenic tubulin peptide) sharing same Fv as IgA
Components
  • Fab fragment of IMMUNOGLOBULIN G1 HEAVY CHAIN
  • Fab fragment of IMMUNOGLOBULIN G1 LIGHT CHAIN
  • peptide from Tubulin beta chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


odontoblast differentiation / cytoskeleton-dependent intracellular transport / GTPase activating protein binding / natural killer cell mediated cytotoxicity / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / microtubule-based process / intercellular bridge / spindle assembly ...odontoblast differentiation / cytoskeleton-dependent intracellular transport / GTPase activating protein binding / natural killer cell mediated cytotoxicity / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / microtubule-based process / intercellular bridge / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / mitotic spindle / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / cell body / Potential therapeutics for SARS / microtubule / cytoskeleton / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain ...Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsTrajtenberg, F. / Correa, A. / Buschiazzo, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of a human IgA1 Fab fragment at 1.55 angstrom resolution: potential effect of the constant domains on antigen-affinity modulation
Authors: Correa, A. / Trajtenberg, F. / Obal, G. / Pritsch, O. / Dighiero, G. / Oppezzo, P. / Buschiazzo, A.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab fragment of IMMUNOGLOBULIN G1 LIGHT CHAIN
B: Fab fragment of IMMUNOGLOBULIN G1 HEAVY CHAIN
C: peptide from Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4574
Polymers48,3653
Non-polymers921
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-21 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.370, 66.450, 137.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab fragment of IMMUNOGLOBULIN G1 LIGHT CHAIN


Mass: 24009.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human)
#2: Antibody Fab fragment of IMMUNOGLOBULIN G1 HEAVY CHAIN


Mass: 23200.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human)
#3: Protein/peptide peptide from Tubulin beta chain / Tubulin beta-5 chain


Mass: 1155.079 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Standard peptide synthesis. The sequence occurs in several species, such as human, mouse, horse, rat, amphibians, etc.
References: UniProt: P07437
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Na citrate, 20% isopropanol, 16% PEG 4000, pH 5.5, vapor diffusion, sitting 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: Dec 14, 2009
RadiationMonochromator: Varimax-HF multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→68.84 Å / Num. all: 25641 / Num. obs: 25641 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 37.93 Å2 / Rsym value: 0.074 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.323.40.5860.4931.61259336880.3120.5860.4932.6100
2.32-2.463.40.4480.3772.11199834900.2380.4480.3773.4100
2.46-2.633.50.3070.25931128832590.1630.3070.2594.9100
2.63-2.843.50.2010.174.61067530850.1070.2010.177.2100
2.84-3.113.50.1240.1047.5985028310.0650.1240.10410.8100
3.11-3.483.50.0710.0612.9894625760.0370.0710.0617.9100
3.48-4.023.50.0470.0419.2789922830.0250.0470.0426.5100
4.02-4.923.40.0340.02924.6682219830.0180.0340.02935.5100
4.92-6.963.40.0340.02923.8523215470.0180.0340.02933.8100
6.96-28.2063.20.0250.02130.828408990.0140.0250.02142.298.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
AMoREphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QO0

3qo0


Resolution: 2.2→28.21 Å / Cor.coef. Fo:Fc: 0.9289 / Cor.coef. Fo:Fc free: 0.9004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: TLS refinement was performed
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1203 4.7 %RANDOM
Rwork0.1964 ---
all0.1982 25593 --
obs0.1982 25593 99.91 %-
Displacement parametersBiso max: 115.51 Å2 / Biso mean: 34.7038 Å2 / Biso min: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.5173 Å20 Å20 Å2
2---3.6936 Å20 Å2
3----2.8237 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 6 104 3322
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1106SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes482HARMONIC5
X-RAY DIFFRACTIONt_it3292HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion439SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3681SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3292HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4470HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion18.29
LS refinement shellResolution: 2.2→2.29 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2333 139 4.88 %
Rwork0.2069 2712 -
all0.2081 2851 -
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)
11.6028-0.19-0.70570.26280.13341.07240.0348-0.0529-0.2443-0.0474-0.06710.05540.0161-0.07910.0323-0.0585-0.0207-0.0182-0.11450.0235-0.0055-21.607-1.9302-26.4066
20.77720.243-0.49130.3702-0.29241.68960.0522-0.164500.0248-0.03950.0004-0.10990.0251-0.0127-0.04210.006-0.011-0.078-0.0131-0.024-11.51457.6375-14.275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|219 }A1 - 219
2X-RAY DIFFRACTION2{ B|2 - B|102 B|108 - B|133 B|140 - B|220 }B2 - 220

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