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- PDB-4yo0: Crystal structure of monoclonal anti-human podoplanin antibody NZ... -

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Basic information

Entry
Database: PDB / ID: 4yo0
TitleCrystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA peptide
Components
  • Heavy chain of antigen binding fragment, Fab
  • Light chain of antigen binding fragment, Fab
  • PA14 peptide
KeywordsIMMUNE SYSTEM / Antibodies / Monoclonal / Antibody Affinity / Chromatography / Affinity / Epitopes / Rats / Immunoglobulin Fab Fragments / Kinetics / Peptides / Protein Binding / Proteins / Recombinant Fusion Proteins / Human podoplanin
Function / homology
Function and homology information


regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / actin-mediated cell contraction / chemokine binding / positive regulation of extracellular matrix disassembly / Specification of primordial germ cells / lymphangiogenesis / regulation of lamellipodium morphogenesis ...regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / actin-mediated cell contraction / chemokine binding / positive regulation of extracellular matrix disassembly / Specification of primordial germ cells / lymphangiogenesis / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / filopodium membrane / wound healing, spreading of cells / anchoring junction / microvillus membrane / lamellipodium membrane / Rho protein signal transduction / lymph node development / positive regulation of epithelial to mesenchymal transition / GPVI-mediated activation cascade / ruffle / cell projection / filopodium / lung development / platelet activation / ruffle membrane / cell junction / cell migration / lamellipodium / regulation of cell shape / 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 / membrane / plasma membrane / cytosol
Similarity search - Function
: / Podoplanin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsFujii, Y. / Kitago, Y. / Arimori, T. / Takagi, J.
CitationJournal: J.Cell.Sci. / Year: 2016
Title: Tailored placement of a turn-forming PA tag into the structured domain of a protein to probe its conformational state
Authors: Fujii, Y. / Matsunaga, Y. / Arimori, T. / Kitago, Y. / Ogasawara, S. / Kaneko, M.K. / Kato, Y. / Takagi, J.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 2.0Feb 5, 2020Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 8, 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 2.2Nov 20, 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
A: Heavy chain of antigen binding fragment, Fab
B: Light chain of antigen binding fragment, Fab
C: Heavy chain of antigen binding fragment, Fab
D: Light chain of antigen binding fragment, Fab
E: PA14 peptide
F: PA14 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8627
Polymers104,8006
Non-polymers621
Water8,989499
1
A: Heavy chain of antigen binding fragment, Fab
B: Light chain of antigen binding fragment, Fab
E: PA14 peptide


Theoretical massNumber of molelcules
Total (without water)52,4003
Polymers52,4003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-31 kcal/mol
Surface area19100 Å2
MethodPISA
2
C: Heavy chain of antigen binding fragment, Fab
D: Light chain of antigen binding fragment, Fab
F: PA14 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4624
Polymers52,4003
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-27 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 80.010, 132.520
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25560.020 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


Mass: 25494.350 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/peptide PA14 peptide


Mass: 1345.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YL7*PLUS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.56→40 Å / Num. obs: 121358 / % possible obs: 97.2 % / Redundancy: 7.5 % / Rsym value: 0.057 / Net I/σ(I): 17.5
Reflection shellResolution: 1.56→1.65 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.5 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YNY

4yny


Resolution: 1.56→40 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.67
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 6035 4.98 %RANDOM
Rwork0.1791 ---
obs0.1808 121132 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.56→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6441 0 4 499 6944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186755
X-RAY DIFFRACTIONf_angle_d1.5049230
X-RAY DIFFRACTIONf_dihedral_angle_d15.0444072
X-RAY DIFFRACTIONf_chiral_restr0.11048
X-RAY DIFFRACTIONf_plane_restr0.0111185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.57770.43211660.38123118X-RAY DIFFRACTION81
1.5777-1.59630.33681830.32143550X-RAY DIFFRACTION90
1.5963-1.61580.3181730.30363839X-RAY DIFFRACTION97
1.6158-1.63620.32092170.29083791X-RAY DIFFRACTION97
1.6362-1.65770.29052040.2713770X-RAY DIFFRACTION97
1.6577-1.68040.30681910.26253864X-RAY DIFFRACTION97
1.6804-1.70450.28592000.24353832X-RAY DIFFRACTION98
1.7045-1.72990.27961980.24163778X-RAY DIFFRACTION97
1.7299-1.75690.25842040.23393889X-RAY DIFFRACTION98
1.7569-1.78570.23711970.21363753X-RAY DIFFRACTION97
1.7857-1.81650.26022070.20663888X-RAY DIFFRACTION98
1.8165-1.84960.22792030.20343829X-RAY DIFFRACTION98
1.8496-1.88510.23212020.19523835X-RAY DIFFRACTION98
1.8851-1.92360.23972060.19083899X-RAY DIFFRACTION98
1.9236-1.96540.2462010.19123836X-RAY DIFFRACTION98
1.9654-2.01120.22992060.19033914X-RAY DIFFRACTION98
2.0112-2.06140.2161990.19093809X-RAY DIFFRACTION99
2.0614-2.11720.25442050.18663903X-RAY DIFFRACTION99
2.1172-2.17950.23752040.18243852X-RAY DIFFRACTION99
2.1795-2.24980.21852050.18123903X-RAY DIFFRACTION99
2.2498-2.33020.22952040.18613924X-RAY DIFFRACTION99
2.3302-2.42350.19522060.19233893X-RAY DIFFRACTION99
2.4235-2.53380.24012060.19173909X-RAY DIFFRACTION99
2.5338-2.66730.24112080.18973945X-RAY DIFFRACTION99
2.6673-2.83440.20582060.18363926X-RAY DIFFRACTION99
2.8344-3.05320.23262070.18413926X-RAY DIFFRACTION100
3.0532-3.36030.20362070.18123933X-RAY DIFFRACTION100
3.3603-3.84620.18442090.15493973X-RAY DIFFRACTION100
3.8462-4.84450.17562090.12953961X-RAY DIFFRACTION100
4.8445-40.01810.16972020.15433855X-RAY DIFFRACTION95
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)
13.403-0.14271.65532.1949-0.04172.175-0.1705-0.3238-0.12040.08330.16720.1207-0.1105-0.12260.00590.1830.02120.0490.17630.03680.1862-52.707413.2613-55.4384
23.5902-0.8042-0.61833.90450.0536.4216-0.0769-0.1534-0.12970.29860.08140.02520.6283-0.1531-0.01630.48950.0222-0.00570.27970.01560.1952-44.035333.8134-33.2712
31.463-0.6438-0.11617.04480.68891.2317-0.026-0.0470.00290.05510.10150.40430.0621-0.0984-0.06720.23190.0073-0.00530.17460.03050.1966-63.359631.7487-64.2808
44.1806-1.47982.38265.0509-1.26196.5366-0.2458-0.07830.29630.2304-0.0629-0.6928-0.75080.3420.2950.527-0.0436-0.0370.29280.06670.2902-39.593948.0531-40.8213
51.86991.61350.42594.28811.7883.2186-0.30170.20760.275-0.6450.23360.3051-0.2898-0.02060.01410.2542-0.0174-0.04550.16430.02990.2832-27.619825.815-8.6946
64.3853-0.27170.84464.77-0.16015.13460.1889-0.1721-0.4156-0.95380.3020.9421-0.5133-0.5107-0.40830.58220.0124-0.12710.35010.12220.4614-38.1117.3409-28.4102
72.02180.68110.04276.48930.8940.6703-0.0112-0.1848-0.01520.54240.0465-0.14790.006-0.055-0.02970.22550.0144-0.00850.16210.01320.1872-27.26237.49645.0722
82.85270.17892.68842.8905-0.37315.58440.30240.0654-0.5689-0.94570.38930.42810.2857-0.2282-0.62680.5985-0.0285-0.20510.34440.06510.5088-30.6634-7.6868-28.7994
97.48653.7129-5.27445.8428-2.42098.2401-0.06640.2241-0.561-0.36950.0180.8842-0.1598-0.98440.07630.22290.0129-0.05450.23510.0170.4387-67.276610.9532-64.9584
104.8024-4.56420.32994.91070.93762.7246-0.201-0.54780.35170.9364-0.00930.26640.0722-0.53170.20530.32770.01480.02070.2265-0.04680.3522-29.272328.94827.9986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 20:137)
2X-RAY DIFFRACTION2(chain A and resseq 138:235)
3X-RAY DIFFRACTION3(chain B and resseq 20:130)
4X-RAY DIFFRACTION4(chain B and resseq 131:229)
5X-RAY DIFFRACTION5(chain C and resseq 20:137)
6X-RAY DIFFRACTION6(chain C and resseq 138:235)
7X-RAY DIFFRACTION7(chain D and resseq 20:130)
8X-RAY DIFFRACTION8(chain D and resseq 131:229)
9X-RAY DIFFRACTION9(chain E and resseq 3:14)
10X-RAY DIFFRACTION10(chain F and resseq 4:14)

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