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- PDB-6lz4: Crystal structure of PMab-1 Fv-clasp fragment with its antigen peptide -

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Basic information

Entry
Database: PDB / ID: 6lz4
TitleCrystal structure of PMab-1 Fv-clasp fragment with its antigen peptide
Components
  • MAP peptide
  • PMab-1 VH(S112C)-SARAH Chimera
  • PMab-1 VL-SARAH(S37C) Chimera
KeywordsIMMUNE SYSTEM / antibody fragment / Fv-clasp
Function / homology
Function and homology information


tube morphogenesis / regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / GPVI-mediated activation cascade / leading edge of lamellipodium / visceral serous pericardium development / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / lymphangiogenesis ...tube morphogenesis / regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / GPVI-mediated activation cascade / leading edge of lamellipodium / visceral serous pericardium development / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / positive regulation of platelet activation / filopodium membrane / positive regulation of cell motility / anchoring junction / wound healing, spreading of cells / microvillus membrane / prostaglandin metabolic process / lung alveolus development / regulation of G1/S transition of mitotic cell cycle / lamellipodium membrane / Rho protein signal transduction / lymph node development / regulation of cell adhesion / positive regulation of epithelial to mesenchymal transition / ruffle / filopodium / lung development / cell-cell adhesion / ruffle membrane / cell migration / lamellipodium / regulation of cell shape / cytoplasmic vesicle / basolateral plasma membrane / cell population proliferation / cell adhesion / positive regulation of cell migration / membrane raft / apical plasma membrane / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / negative regulation of apoptotic process / signal transduction / plasma membrane / cytosol
Similarity search - Function
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsArimori, T. / Takagi, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)19am0101075 Japan
Japan Society for the Promotion of Science (JSPS)A17H068390 Japan
CitationJournal: J.Biochem. / Year: 2020
Title: Site-specific epitope insertion into recombinant proteins using the MAP tag system.
Authors: Wakasa, A. / Kaneko, M.K. / Kato, Y. / Takagi, J. / Arimori, T.
History
DepositionFeb 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PMab-1 VH(S112C)-SARAH Chimera
B: PMab-1 VL-SARAH(S37C) Chimera
C: MAP peptide
D: PMab-1 VH(S112C)-SARAH Chimera
E: PMab-1 VL-SARAH(S37C) Chimera
F: MAP peptide


Theoretical massNumber of molelcules
Total (without water)78,0226
Polymers78,0226
Non-polymers00
Water00
1
A: PMab-1 VH(S112C)-SARAH Chimera
B: PMab-1 VL-SARAH(S37C) Chimera
C: MAP peptide


Theoretical massNumber of molelcules
Total (without water)39,0113
Polymers39,0113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-49 kcal/mol
Surface area16590 Å2
MethodPISA
2
D: PMab-1 VH(S112C)-SARAH Chimera
E: PMab-1 VL-SARAH(S37C) Chimera
F: MAP peptide


Theoretical massNumber of molelcules
Total (without water)39,0113
Polymers39,0113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-48 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.652, 85.088, 115.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody PMab-1 VH(S112C)-SARAH Chimera


Mass: 19156.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The VH domain region (residues 1-113) of this chimeric protein is derived from Rattus norvegicus, while the SARAH domain region (residues 114-164) is derived from Homo sapiens.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli)
#2: Antibody PMab-1 VL-SARAH(S37C) Chimera


Mass: 18424.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The VL domain region (residues 1-108) of this chimeric protein is derived from Rattus norvegicus, while the SARAH domain region (residues 109-159) is derived from Homo sapiens.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide MAP peptide


Mass: 1429.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q62011*PLUS
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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.49→48.15 Å / Num. obs: 23798 / % possible obs: 99.3 % / Redundancy: 8.7 % / Biso Wilson estimate: 61.08 Å2 / CC1/2: 0.998 / Rsym value: 0.13 / Net I/σ(I): 11.55
Reflection shellResolution: 2.49→2.64 Å / Num. unique obs: 3645 / CC1/2: 0.65 / Rsym value: 1.42

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LK3, 5W5Z, 5XCT

1lk3

5w5z

5xct


Resolution: 2.49→42.54 Å / SU ML: 0.4411 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.0949 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 1190 5 %
Rwork0.2448 22597 -
obs0.246 23787 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.66 Å2
Refinement stepCycle: LAST / Resolution: 2.49→42.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5175 0 0 0 5175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515289
X-RAY DIFFRACTIONf_angle_d0.82977164
X-RAY DIFFRACTIONf_chiral_restr0.0449780
X-RAY DIFFRACTIONf_plane_restr0.0059915
X-RAY DIFFRACTIONf_dihedral_angle_d7.94533185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.590.40411260.39542342X-RAY DIFFRACTION94.31
2.59-2.710.36291300.36332488X-RAY DIFFRACTION99.81
2.71-2.850.37881300.35132479X-RAY DIFFRACTION99.92
2.85-3.030.35851320.33562498X-RAY DIFFRACTION99.92
3.03-3.270.32211320.30252499X-RAY DIFFRACTION99.77
3.27-3.590.27461320.272513X-RAY DIFFRACTION99.77
3.59-4.110.26821330.22862521X-RAY DIFFRACTION99.85
4.11-5.180.23311350.18992579X-RAY DIFFRACTION99.96
5.18-42.540.21621400.20372678X-RAY DIFFRACTION99.82
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)
11.849987322110.981496979580.4879976800682.614544918821.867434313375.327026710460.0732327584824-0.158869499094-0.5840490307550.3136952700340.153109527347-0.3277480868681.142236094980.0541382821529-0.3036336327570.61543911870.0605714382483-0.09320906597480.3606490310180.06542997622520.5942863620944.06820683103-14.2671416275-0.606885970296
21.77903587577-1.87998498914-1.70325031473.350297640921.56144248733.82496260439-0.00468639259255-0.0224732751234-0.128394488185-0.08992712836030.29948774491-0.198877611442-0.04590056553821.05056658733-0.1699202827560.596017213407-0.0453678700077-0.0627394303110.860441193612-0.1030667554920.5298691224125.60104540477.84339309667-12.0377248031
32.0619775671-0.120770433497-0.2773139507565.920912711370.09197041638354.07699929381-0.0504514686853-0.2370516146670.1019389359410.0517006244885-0.06797867617290.7058937108430.109995295983-0.5331684428530.1555997305080.2539652508220.0320603780120.00651594050840.451044435435-0.02561060963890.391801711661-7.734683354864.35569071851.95487156332
42.68785231461-1.25945053452-1.827093203434.121143044292.803795498066.88141572674-0.3629701826070.0937436901473-0.417148840609-0.06026730343460.08967959826390.3268174905640.3588707569770.5415444031870.2670775799310.396385783255-0.0511626022729-0.02674735256870.577599326204-0.01316951309220.46557855145516.56347279698.86967200188-4.21549379579
53.92451900281-1.387807642641.299839812925.89970395229-2.224658435115.22327698290.5175529710560.256519537019-0.0148525013051-0.700149133306-0.43197785557-0.4344464254780.1970646729150.888509767181-0.1441004441810.813090119787-0.05284034123690.06391631587960.5364163598610.02186651591190.469790988497-1.43775137264-31.1966527543-27.8305688959
65.49758869187-3.475875382582.360333300384.50846336697-3.430691569483.929671150510.006959348246790.2301955548550.157641119567-0.2797894158750.1246850547480.1479624093080.246124257401-0.183691599967-0.02581562398670.519579285583-0.07508560775330.03304550673870.5415185948170.02038870476780.480116863405-22.4497692432-51.7596639729-15.8239379474
74.34846137481-1.884746555353.863254163273.85318077136-1.636784693426.771411226550.211333561177-0.4858350039610.3505097213030.4203928453730.07121429489910.23334517965-0.919820953883-1.26491889985-0.3296287708111.017231350740.1861312449230.1821111243770.7358690067740.07873510408410.507618017089-19.0028237743-17.6356280644-31.3769248899
83.277030850190.4304450536990.9220530046491.84036962834-1.939827682523.40376793881-0.3275406045751.162807521260.8061368701890.224463729049-0.0386493471726-0.093085335484-0.2377983469280.1625197263080.1081539870310.350370307503-0.02144075563090.03379098671490.6610924780470.05522958030130.551728216268-19.1834020853-45.0224409029-21.9807856559
93.044179288094.613629963860.4594185639996.995471027120.7173939809810.0925947772502-0.356851168666-0.08198115180360.4403460894270.1771279283170.1434010808240.27213475883-0.129740649759-0.4406049376690.1036604082810.726589208515-0.1365400552790.07432383264970.542127142636-0.06449815377970.682457105737-11.337602667-12.07576155954.31165285855
100.06802832699050.872571295667-0.4363763505518.56421979617-4.368393057772.24353529172-0.0200054655245-0.0110582259715-0.433685981010.5233376020780.0706437890577-0.47259477104-0.0939053460802-0.157936580016-0.04270988600690.794929259941-0.05433034754060.157286303740.618666308920.09868914706880.547523173908-3.14001530198-17.1674998867-34.4648190453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 164)
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 108 )
4X-RAY DIFFRACTION4chain 'B' and (resid 109 through 158 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 113 )
6X-RAY DIFFRACTION6chain 'D' and (resid 117 through 163 )
7X-RAY DIFFRACTION7chain 'E' and (resid 1 through 106 )
8X-RAY DIFFRACTION8chain 'E' and (resid 119 through 159 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 8 )
10X-RAY DIFFRACTION10chain 'F' and (resid 1 through 7 )

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