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- PDB-2zpk: Crystal structure of P20.1 Fab fragment in complex with its antig... -

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Basic information

Entry
Database: PDB / ID: 2zpk
TitleCrystal structure of P20.1 Fab fragment in complex with its antigen peptide
Components
  • IgG1-lambda P20.1 Fab (heavy chain)
  • IgG1-lambda P20.1 Fab (light chain)
  • Proteinase-activated receptor 4
KeywordsIMMUNE SYSTEM / mouse IgG Fab fragment in complex with antigen peptide
Function / homology
Function and homology information


thrombin-activated receptor activity / platelet dense granule organization / positive regulation of Rho protein signal transduction / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / G protein-coupled receptor activity / platelet aggregation / platelet activation / response to wounding / blood coagulation ...thrombin-activated receptor activity / platelet dense granule organization / positive regulation of Rho protein signal transduction / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / G protein-coupled receptor activity / platelet aggregation / platelet activation / response to wounding / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / protease binding / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Protease-activated receptor 4 / Protease-activated receptor / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Proteinase-activated receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNogi, T. / Sanagawa, T. / Takagi, J.
CitationJournal: Protein Sci. / Year: 2008
Title: Novel affinity tag system using structurally defined antibody-tag interaction: application to single-step protein purification
Authors: Nogi, T. / Sangawa, T. / Tabata, S. / Nagae, M. / Tamura-Kawakami, K. / Beppu, A. / Hattori, M. / Yasui, N. / Takagi, J.
History
DepositionJul 16, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IgG1-lambda P20.1 Fab (light chain)
H: IgG1-lambda P20.1 Fab (heavy chain)
P: Proteinase-activated receptor 4
M: IgG1-lambda P20.1 Fab (light chain)
I: IgG1-lambda P20.1 Fab (heavy chain)
Q: Proteinase-activated receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3729
Polymers94,0956
Non-polymers2763
Water7,963442
1
L: IgG1-lambda P20.1 Fab (light chain)
H: IgG1-lambda P20.1 Fab (heavy chain)
P: Proteinase-activated receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1404
Polymers47,0483
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-31 kcal/mol
Surface area18440 Å2
MethodPISA
2
M: IgG1-lambda P20.1 Fab (light chain)
I: IgG1-lambda P20.1 Fab (heavy chain)
Q: Proteinase-activated receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2325
Polymers47,0483
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-33 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.045, 65.271, 85.030
Angle α, β, γ (deg.)99.93, 93.50, 96.46
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody IgG1-lambda P20.1 Fab (light chain)


Mass: 22933.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody IgG1-lambda P20.1 Fab (heavy chain)


Mass: 23240.305 Da / Num. of mol.: 2 / Fragment: Variable and Constant region / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Protein/peptide Proteinase-activated receptor 4 / PAR-4 / Thrombin receptor-like 3 / Coagulation factor II receptor-like 3


Mass: 873.976 Da / Num. of mol.: 2 / Fragment: UNP residues 46-53 / Source method: obtained synthetically
Details: This sequence occurs in the N-terminal region of human protease-activated receptor 4.
References: UniProt: Q96RI0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF ENTITY 1 (AB447555) AND 2 (AB447554) HAVE BEEN DEPOSITED TO DDBJ.

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20-23% (wt/vol) PEG 3000, 0.1M Sodium acetate (pH4.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DIP-6040 / Detector: IMAGE PLATE / Date: Dec 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→46.78 Å / Num. obs: 76301 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 21.64 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.2 / Num. unique all: 10894 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NC4

1nc4


Resolution: 1.8→46.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.002 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3774 4.9 %RANDOM
Rwork0.1719 ---
obs0.1735 72513 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0.58 Å2-0.8 Å2
2---0.28 Å20.8 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6441 0 18 442 6901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226922
X-RAY DIFFRACTIONr_angle_refined_deg1.471.959525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6765917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5724.145234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.785151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9411520
X-RAY DIFFRACTIONr_chiral_restr0.0990.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025238
X-RAY DIFFRACTIONr_nbd_refined0.20.22865
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2433
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.217
X-RAY DIFFRACTIONr_mcbond_it0.7581.54561
X-RAY DIFFRACTIONr_mcangle_it1.22327320
X-RAY DIFFRACTIONr_scbond_it1.94132745
X-RAY DIFFRACTIONr_scangle_it2.9534.52203
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 271 -
Rwork0.201 5211 -
obs-5482 94.5 %
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)
14.06940.0730.83842.2443-0.04730.8707-0.039-0.0790.0017-0.01540.0110.03730.0099-0.06790.028-0.22560.02320.0122-0.1782-0.0022-0.158120.5038-4.651253.475
21.6005-1.9319-0.07195.52990.02730.52370.01460.0306-0.06830.0739-0.04670.0772-0.064-0.04980.0321-0.11320.02150.0001-0.1651-0.0046-0.135425.923426.781350.463
32.12740.05180.05223.5276-1.52242.64530.03360.1544-0.0251-0.23730.04690.01440.1139-0.0843-0.0805-0.15790.0053-0.0086-0.1369-0.0314-0.13649.4994-1.41934.7773
44.45210.1011.73633.23640.14424.7819-0.1767-0.12330.16530.05530.1219-0.182-0.15910.22190.0548-0.11710.026-0.0264-0.1841-0.0078-0.115429.896827.648734.5934
52.927-0.4777.04397.293110.06534.3760.0231-0.664-0.45680.61090.04680.06622.0749-0.4325-0.06990.0391-0.0267-0.0171-0.05620.00150.0586.3803-16.485946.6509
61.8841.12690.79292.68610.24633.70450.0728-0.1950.05530.2729-0.1774-0.0078-0.26520.0580.1046-0.1171-0.00180.008-0.1561-0.0048-0.154929.3034-13.067973.5812
71.75911.9274-3.86294.333-5.443613.1814-0.05490.14250.1952-0.3490.63770.5282-0.0385-1.4967-0.5828-0.0321-0.0134-0.030.14160.1-0.007912.5687-41.902784.7948
82.21141.3457-0.58242.8861-0.62355.01710.069-0.2145-0.03810.2527-0.1169-0.0751-0.10440.26450.0479-0.0246-0.0588-0.0485-0.03320.021-0.095539.639-18.19592.495
92.28011.28291.72245.8036-0.02857.3169-0.0740.2796-0.0937-0.3035-0.0448-0.1810.23770.20160.1188-0.1239-0.02210.0428-0.05320.0262-0.110224.541-48.119393.8664
1031.5804-19.371817.813821.9623-10.353910.0810.02121.1051.3423-0.9109-0.8699-1.0527-0.6960.87870.84880.1634-0.1695-0.0250.11130.08230.004244.2829-3.048481.0185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1081 - 110
2X-RAY DIFFRACTION2LA109 - 210111 - 212
3X-RAY DIFFRACTION3HB1 - 1131 - 116
4X-RAY DIFFRACTION4HB114 - 213117 - 216
5X-RAY DIFFRACTION5PC1 - 81 - 8
6X-RAY DIFFRACTION6MD2 - 1082 - 110
7X-RAY DIFFRACTION7MD109 - 208111 - 210
8X-RAY DIFFRACTION8IE1 - 1131 - 116
9X-RAY DIFFRACTION9IE114 - 212117 - 215
10X-RAY DIFFRACTION10QF1 - 81 - 8

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