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

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Basic information

Entry
Database: PDB / ID: 7cqc
TitleThe NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184
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: 2.5 Å
AuthorsAruga, R. / Tamura-Sakaguchi, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 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


Theoretical massNumber of molelcules
Total (without water)67,8933
Polymers67,8933
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-30 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.358, 75.203, 172.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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


Mass: 23409.316 Da / Num. of mol.: 1
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.: 1
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: 21135.703 Da / Num. of mol.: 1 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20%(wt./vol.) PEG 3350, 0.2 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→45.68 Å / Num. obs: 47746 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2685 / CC1/2: 0.674

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Processing

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

4yoo

3wkl


Resolution: 2.5→42.97 Å / SU ML: 0.4623 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 34.1829 / Stereochemistry target values: GeoStd + Monomer Library
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2575 2219 4.87 %
Rwork0.2302 43308 -
obs0.2316 45527 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 0 50 4740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244793
X-RAY DIFFRACTIONf_angle_d0.53966513
X-RAY DIFFRACTIONf_chiral_restr0.0425743
X-RAY DIFFRACTIONf_plane_restr0.0043831
X-RAY DIFFRACTIONf_dihedral_angle_d9.2172876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.45731520.36292599X-RAY DIFFRACTION98.21
2.55-2.610.40361230.35072791X-RAY DIFFRACTION99.93
2.61-2.680.42371300.35392679X-RAY DIFFRACTION100
2.68-2.750.41841200.33782765X-RAY DIFFRACTION99.97
2.75-2.830.36071630.31072649X-RAY DIFFRACTION99.86
2.83-2.920.37291430.30212734X-RAY DIFFRACTION100
2.92-3.030.40081450.30082670X-RAY DIFFRACTION99.82
3.03-3.150.36081360.29972751X-RAY DIFFRACTION99.93
3.15-3.290.32961170.28022731X-RAY DIFFRACTION100
3.29-3.460.29291680.26362674X-RAY DIFFRACTION99.82
3.46-3.680.28181220.23732743X-RAY DIFFRACTION99.83
3.68-3.960.25881320.22682710X-RAY DIFFRACTION99.89
3.96-4.360.21521260.18832741X-RAY DIFFRACTION99.83
4.36-4.990.15691220.1662704X-RAY DIFFRACTION99.86
4.99-6.290.24261660.19132678X-RAY DIFFRACTION99.89
6.29-42.970.17551540.18722689X-RAY DIFFRACTION99.27

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