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- PDB-3qo0: Monoclinic form of IgG1 Fab fragment (in complex with antigenic p... -

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Basic information

Entry
Database: PDB / ID: 3qo0
TitleMonoclinic form of IgG1 Fab fragment (in complex with antigenic 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 / sperm principal piece / intercellular bridge / nuclear envelope lumen / regulation of synapse organization / sperm end piece / MHC class I protein binding ...odontoblast differentiation / cytoskeleton-dependent intracellular transport / GTPase activating protein binding / natural killer cell mediated cytotoxicity / sperm principal piece / intercellular bridge / nuclear envelope lumen / regulation of synapse organization / sperm end piece / MHC class I protein binding / ciliary tip / microtubule-based process / 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 / mitotic spindle / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / azurophil granule lumen / mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / cilium / cell body / microtubule / Potential therapeutics for SARS / cytoskeleton / cell division / membrane raft / protein domain specific binding / ubiquitin protein ligase binding / GTPase activity / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
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 / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsTrajtenberg, F. / Correa-Bove, A. / Buschiazzo, A.
CitationJournal: To be published
Title: Crystal structures of human IGA1 and IGG1 fab fragments sharing the same variable domains
Authors: Trajtenberg, F. / Correa-Bove, A. / 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 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)49,7755
Polymers49,5913
Non-polymers1842
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-22 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.320, 67.270, 68.880
Angle α, β, γ (deg.)90.000, 103.100, 90.000
Int Tables number4
Space group name H-MP1211

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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: 2381.284 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1M Na citrate, 20% isopropanol, 16% PEG 4000, pH 6.1, 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 4, 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: 2.3→28.232 Å / Num. all: 21241 / Num. obs: 21241 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40.76 Å2 / Rsym value: 0.097 / Net I/σ(I): 12.4
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
2.3-2.423.60.6720.5721.41122030790.3490.6720.5722.4100
2.42-2.573.70.510.4351.81075029270.2650.510.4353100
2.57-2.753.70.3590.3062.51012427470.1860.3590.3064.3100
2.75-2.973.70.240.2053.8943125490.1240.240.2056.2100
2.97-3.253.70.1420.1216.5873323420.0730.1420.12110.1100
3.25-3.643.70.0820.0711.1799521380.0420.0820.0716.9100
3.64-4.23.70.0590.0515.1713919040.030.0590.0523.7100
4.2-5.143.70.0410.03520.3598216000.0210.0410.03532100
5.14-7.273.70.0460.03918.8468112560.0230.0460.03927.5100
7.27-28.2323.60.0270.02329.725186990.0140.0270.02341.698.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
FFTphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→28.23 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9076 / Occupancy max: 1 / Occupancy min: 1 / 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
Rfree0.2214 1010 4.76 %RANDOM
Rwork0.1688 ---
all0.1712 21224 --
obs0.1712 21224 99.93 %-
Displacement parametersBiso max: 102.53 Å2 / Biso mean: 33.3728 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1-3.9761 Å20 Å2-0.8879 Å2
2---0.4797 Å20 Å2
3----3.4964 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 12 227 3548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013388HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.284598HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1144SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes495HARMONIC5
X-RAY DIFFRACTIONt_it3388HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion20.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
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_contact3890SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.41 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2802 137 4.89 %
Rwork0.2023 2663 -
all0.206 2800 -
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)
11.54440.29280.19450.2069-0.45231.92640.05690.0377-0.0245-0.0565-0.12470.02360.10010.19380.0679-0.05530.03710.0044-0.006-0.0237-0.000126.7536-5.32312.7695
22.14950.0619-0.57831.50720.25910.86640.0191-0.0654-0.11340.1383-0.0351-0.07820.03210.02790.016-0.0374-0.01960.0024-0.01660.0198-0.052-0.0625-4.518739.5541
31.4699-0.3044-0.87851.1738-0.07821.6916-0.00520.24660.2015-0.109-0.0045-0.07580.0552-0.04550.0097-0.0777-0.0146-0.03170.0140.0272-0.00619.01522.08590.5751
41.55310.29060.66031.15030.63471.9380.0183-0.1139-0.02190.0393-0.05-0.0999-0.1435-0.10230.0316-0.0338-0.0110.0113-0.06040.0278-0.0205-1.53718.018330.0162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|114 }A1 - 114
2X-RAY DIFFRACTION2{ A|115 - A|219 }A115 - 219
3X-RAY DIFFRACTION3{ B|1 - B|119 }B1 - 119
4X-RAY DIFFRACTION4{ B|120 - B|220 }B120 - 220

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