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- PDB-7cqd: The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicu... -

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Basic information

Entry
Database: PDB / ID: 7cqd
TitleThe NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 235 and 236
Components
  • Heavy chain of antigen binding fragment, Fab of NZ-1
  • Light chain of antigen binding fragment, Fab of NZ-1
  • Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964
KeywordsHYDROLASE/IMMUNE SYSTEM / soluble domain / Fab complex / MEMBRANE PROTEIN / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / chemokine binding / Specification of primordial germ cells / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis ...regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / chemokine binding / Specification of primordial germ cells / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / filopodium membrane / wound healing, spreading of cells / anchoring junction / microvillus membrane / lamellipodium membrane / lymph node development / positive regulation of epithelial to mesenchymal transition / GPVI-mediated activation cascade / Rho protein signal transduction / ruffle / lung development / cell projection / filopodium / metalloendopeptidase activity / platelet activation / ruffle membrane / cell junction / cell migration / regulation of cell shape / lamellipodium / protein-folding chaperone binding / cytoplasmic vesicle / basolateral plasma membrane / cell adhesion / positive regulation of cell migration / apical plasma membrane / membrane raft / signaling receptor binding / negative regulation of cell population proliferation / negative regulation of apoptotic process / signal transduction / mitochondrion / proteolysis / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Podoplanin / Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...: / Podoplanin / Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative zinc metalloprotease aq_1964 / Podoplanin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Aquifex aeolicus VF5 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTamura-Sakaguchi, R. / Aruga, R. / Nogi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03170 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion.
Authors: Tamura-Sakaguchi, R. / Aruga, R. / Hirose, M. / Ekimoto, T. / Miyake, T. / Hizukuri, Y. / Oi, R. / Kaneko, M.K. / Kato, Y. / Akiyama, Y. / Ikeguchi, M. / Iwasaki, K. / Nogi, T.
History
DepositionAug 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of antigen binding fragment, Fab of NZ-1
L: Light chain of antigen binding fragment, Fab of NZ-1
A: Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964
M: Light chain of antigen binding fragment, Fab of NZ-1
I: Heavy chain of antigen binding fragment, Fab of NZ-1
B: Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964


Theoretical massNumber of molelcules
Total (without water)136,1646
Polymers136,1646
Non-polymers00
Water00
1
H: Heavy chain of antigen binding fragment, Fab of NZ-1
L: Light chain of antigen binding fragment, Fab of NZ-1
A: Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964


Theoretical massNumber of molelcules
Total (without water)68,0823
Polymers68,0823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Light chain of antigen binding fragment, Fab of NZ-1
I: Heavy chain of antigen binding fragment, Fab of NZ-1
B: Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964


Theoretical massNumber of molelcules
Total (without water)68,0823
Polymers68,0823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.360, 80.175, 168.540
Angle α, β, γ (deg.)90.000, 95.705, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Antibody Heavy chain of antigen binding fragment, Fab of NZ-1


Mass: 23409.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#2: Antibody Light chain of antigen binding fragment, Fab of NZ-1


Mass: 23347.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#3: Protein Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964


Mass: 21324.875 Da / Num. of mol.: 2 / Fragment: PDZ tandem fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: VF5 / Gene: aq_1964 / Production host: Escherichia coli (E. coli) / References: UniProt: O67776, UniProt: Q86YL7
Has ligand of interestN
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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10%(wt/vol) PEG 3350, 0.2 M L-proline, 0.1 M HEPES-Na (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→38.99 Å / Num. obs: 70558 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 89.12 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Net I/σ(I): 8
Reflection shellResolution: 3.2→3.36 Å / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4745 / CC1/2: 0.774

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Processing

Software
NameVersionClassification
PHENIX1.13_2998+SVNrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4yo0, 3wkl

4yo0

3wkl


Resolution: 3.2→38.99 Å / SU ML: 0.428 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 33.5126 / Stereochemistry target values: GeoStd + Monomer Library
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2859 3279 4.87 %
Rwork0.2646 64000 -
obs0.2657 67279 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.44 Å2
Refinement stepCycle: LAST / Resolution: 3.2→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7901 0 0 0 7901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348084
X-RAY DIFFRACTIONf_angle_d0.854410996
X-RAY DIFFRACTIONf_chiral_restr0.05081245
X-RAY DIFFRACTIONf_plane_restr0.00551408
X-RAY DIFFRACTIONf_dihedral_angle_d15.29914850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.43051740.41512735X-RAY DIFFRACTION95.53
3.25-3.30.38811480.38562778X-RAY DIFFRACTION96.86
3.3-3.350.43131280.3762881X-RAY DIFFRACTION97.76
3.35-3.410.36561610.35232801X-RAY DIFFRACTION98.27
3.41-3.470.39011580.34242843X-RAY DIFFRACTION98.33
3.47-3.540.32621220.32992877X-RAY DIFFRACTION98.13
3.54-3.610.28171060.30482814X-RAY DIFFRACTION98.05
3.61-3.690.34211440.31312895X-RAY DIFFRACTION98.06
3.69-3.780.35221340.30772807X-RAY DIFFRACTION97.77
3.78-3.870.36981560.31092820X-RAY DIFFRACTION97.22
3.87-3.970.32741500.29172756X-RAY DIFFRACTION96.74
3.97-4.090.30071410.26172818X-RAY DIFFRACTION96.07
4.09-4.220.24691580.25192756X-RAY DIFFRACTION95.67
4.22-4.370.26681470.22512688X-RAY DIFFRACTION94.15
4.37-4.550.29441400.21922707X-RAY DIFFRACTION93.34
4.55-4.760.22621650.22942717X-RAY DIFFRACTION94.31
4.76-5.010.27961300.21482779X-RAY DIFFRACTION96.52
5.01-5.320.2659880.22362853X-RAY DIFFRACTION97.32
5.32-5.730.27281140.22162885X-RAY DIFFRACTION97.85
5.73-6.30.26281090.24542811X-RAY DIFFRACTION96.98
6.3-7.210.26541390.26462842X-RAY DIFFRACTION97.29
7.21-9.060.25762190.24792609X-RAY DIFFRACTION93.36
9.06-38.990.24571480.25252528X-RAY DIFFRACTION88.29

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