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- PDB-5xcv: Crystal structure of NZ-1 Fv-clasp fragment with its antigen peptide -

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Basic information

Entry
Database: PDB / ID: 5xcv
TitleCrystal structure of NZ-1 Fv-clasp fragment with its antigen peptide
Components
  • PA14 peptide
  • VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
  • VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
KeywordsIMMUNE SYSTEM / antibody fragment / Fv-clasp
Function / homology
Function and homology information


lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / regulation of lamellipodium morphogenesis ...lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / filopodium membrane / anchoring junction / wound healing, spreading of cells / microvillus membrane / lamellipodium membrane / Rho protein signal transduction / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / lymph node development / ruffle / GPVI-mediated activation cascade / filopodium / cell projection / lung development / cell-cell adhesion / ruffle membrane / platelet activation / cell migration / lamellipodium / cell junction / regulation of cell shape / protein-folding chaperone binding / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of cell migration / membrane raft / apical plasma membrane / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of apoptotic process / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Podoplanin / p53, subunit A / p53-like tetramerisation domain / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus (rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 Å
AuthorsArimori, T. / Takagi, J.
CitationJournal: Structure / Year: 2017
Title: Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability
Authors: Arimori, T. / Kitago, Y. / Umitsu, M. / Fujii, Y. / Asaki, R. / Tamura-Kawakami, K. / Takagi, J.
History
DepositionMar 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
B: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
C: PA14 peptide
D: VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
E: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
F: PA14 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6868
Polymers78,6066
Non-polymers802
Water4,432246
1
A: VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
B: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
C: PA14 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3835
Polymers39,3033
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-52 kcal/mol
Surface area16940 Å2
MethodPISA
2
D: VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera
E: VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera
F: PA14 peptide


Theoretical massNumber of molelcules
Total (without water)39,3033
Polymers39,3033
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-59 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.617, 50.122, 121.868
Angle α, β, γ (deg.)90.00, 110.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera


Mass: 19370.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rat), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#2: Antibody VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera


Mass: 18586.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rat), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2M Calcium acetate, 0.1M MES (pH 6.5), 20%(w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 46235 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rsym value: 0.109 / Net I/σ(I): 16.05
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.39 / Rsym value: 0.674 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(dev_2341: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCT, 4YO0

5xct

4yo0


Resolution: 2.143→41.762 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 2235 4.94 %
Rwork0.2284 --
obs0.2307 45272 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.143→41.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 2 246 5486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085341
X-RAY DIFFRACTIONf_angle_d0.9047214
X-RAY DIFFRACTIONf_dihedral_angle_d18.6283228
X-RAY DIFFRACTIONf_chiral_restr0.052779
X-RAY DIFFRACTIONf_plane_restr0.005934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1425-2.18910.36121190.32312360X-RAY DIFFRACTION87
2.1891-2.240.37541450.31212652X-RAY DIFFRACTION99
2.24-2.2960.39491530.29142665X-RAY DIFFRACTION99
2.296-2.35810.31491480.2812670X-RAY DIFFRACTION100
2.3581-2.42750.32061180.28282699X-RAY DIFFRACTION100
2.4275-2.50580.34221610.27232693X-RAY DIFFRACTION100
2.5058-2.59540.35031260.27312709X-RAY DIFFRACTION100
2.5954-2.69930.3331470.2862667X-RAY DIFFRACTION100
2.6993-2.82210.31851540.26292709X-RAY DIFFRACTION100
2.8221-2.97080.34461170.25362753X-RAY DIFFRACTION100
2.9708-3.15690.26791510.24372696X-RAY DIFFRACTION100
3.1569-3.40050.27711370.22782709X-RAY DIFFRACTION100
3.4005-3.74260.24311440.19982727X-RAY DIFFRACTION100
3.7426-4.28370.20751510.18172747X-RAY DIFFRACTION100
4.2837-5.39510.22351260.17022754X-RAY DIFFRACTION100
5.3951-41.770.24191380.2112827X-RAY DIFFRACTION99
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)
12.50390.93610.91072.47311.80754.06190.1001-0.0888-0.09350.0154-0.0490.07960.0782-0.3617-0.04730.43290.00430.01030.1330.04090.2197149.593271.958245.9619
22.55430.68041.00330.59560.39192.25970.36110.0442-0.5094-0.17280.03150.07080.29580.3252-0.33080.4871-0.0529-0.07470.2448-0.0140.3293160.56350.91226.133
33.74860.66490.83454.07270.43014.58320.01040.4148-0.1787-0.12790.1599-0.72950.17270.8092-0.16040.44380.00840.03270.237-0.06230.355171.368184.64340.6302
43.30771.03290.87712.2617-0.51382.1059-0.07390.1451-0.3871-0.43770.1984-0.17580.22720.0923-0.08820.5143-0.01070.01320.1426-0.01830.2493164.172380.16541.5113
58.59090.65485.38991.05080.137.1429-0.0033-0.55630.095-0.0187-0.02970.0835-0.2092-0.0799-0.00380.5402-0.0635-0.00430.22220.01430.222160.263554.650136.1217
63.1675-0.80010.33784.02-0.88261.9795-0.09010.3610.2763-0.1787-0.07360.087-0.5249-0.8780.15670.64270.1927-0.11640.6397-0.00540.2946132.443378.381713.671
75.13090.90512.54840.39810.74463.30250.29020.4198-0.401-0.04970.2073-0.0356-0.00240.1611-0.49390.4642-0.0282-0.0630.23260.04650.2787147.284853.95049.9053
82.840.0391-0.22360.82950.51281.1884-0.1537-0.20450.02680.0887-0.23470.5316-0.1433-0.5317-0.01540.2380.09120.02841.64-0.21710.3915118.617366.67717.1508
99.02722.38125.04851.00411.50674.546-0.16490.53970.30920.02840.18680.1426-0.4017-0.0318-0.01130.4130.0441-0.02140.26080.06090.2551136.722358.03344.6064
100.0503-0.08690.22750.96790.13090.8835-0.1132-0.3211-0.07170.1343-0.12640.4735-0.007-1.16060.20150.491-0.12350.01212.0273-0.25360.5246111.491963.417218.8316
110.8204-0.05481.11020.5618-0.19941.5578-0.1678-0.17520.42780.0842-0.35370.21050.1345-0.15730.41860.47920.00920.00470.2578-0.01550.2788151.41586.774953.3051
120.0465-0.0747-0.03410.15330.05480.02380.06780.1495-0.0247-0.0429-0.0267-0.2451-0.0168-0.02810.02780.25560.2199-0.09310.7251-0.05570.4799118.768186.450815.711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 0:118))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 119:163))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 1:28) or (resseq 50:87))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 29:49) or (resseq 88:106))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 118:158))
6X-RAY DIFFRACTION6chain 'D' and ((resseq 3:118))
7X-RAY DIFFRACTION7chain 'D' and ((resseq 119:164))
8X-RAY DIFFRACTION8chain 'E' and ((resseq 29:49) or (resseq 88:110))
9X-RAY DIFFRACTION9chain 'E' and ((resseq 111:158))
10X-RAY DIFFRACTION10chain 'E' and ((resseq 1:28) or (resseq 50:87))
11X-RAY DIFFRACTION11chain 'C'
12X-RAY DIFFRACTION12chain 'F'

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