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- PDB-8tkt: ZIG-4-INS-6 complex, C-centered monoclinic form -

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Basic information

Entry
Database: PDB / ID: 8tkt
TitleZIG-4-INS-6 complex, C-centered monoclinic form
Components
  • Probable insulin-like peptide beta-type 5
  • Zwei Ig domain protein zig-4
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / NEUROPEPTIDE / SIGNALING PROTEIN / PROTEIN BINDING / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


cellular response to salt / negative regulation of dauer entry / dauer larval development / regulation of synaptic assembly at neuromuscular junction / chemosensory behavior / olfactory learning / neuron development / insulin receptor binding / hormone activity / insulin receptor signaling pathway ...cellular response to salt / negative regulation of dauer entry / dauer larval development / regulation of synaptic assembly at neuromuscular junction / chemosensory behavior / olfactory learning / neuron development / insulin receptor binding / hormone activity / insulin receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Nematode insulin-like peptide, beta type / : / Nematode insulin-related peptide beta type / : / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...Nematode insulin-like peptide, beta type / : / Nematode insulin-related peptide beta type / : / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Zwei Ig domain protein zig-4 / Probable insulin-like peptide beta-type 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCheng, S. / Baltrusaitis, E. / Aziz, Z. / Nawrocka, W.I. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 United States
CitationJournal: Biorxiv / Year: 2024
Title: Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways.
Authors: Nawrocka, W.I. / Cheng, S. / Hao, B. / Rosen, M.C. / Cortes, E. / Baltrusaitis, E.E. / Aziz, Z. / Kovacs, I.A. / Ozkan, E.
History
DepositionJul 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zwei Ig domain protein zig-4
B: Probable insulin-like peptide beta-type 5
C: Zwei Ig domain protein zig-4
D: Probable insulin-like peptide beta-type 5


Theoretical massNumber of molelcules
Total (without water)60,3744
Polymers60,3744
Non-polymers00
Water1267
1
A: Zwei Ig domain protein zig-4
B: Probable insulin-like peptide beta-type 5


Theoretical massNumber of molelcules
Total (without water)30,1872
Polymers30,1872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Zwei Ig domain protein zig-4
D: Probable insulin-like peptide beta-type 5


Theoretical massNumber of molelcules
Total (without water)30,1872
Polymers30,1872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.430, 56.654, 73.685
Angle α, β, γ (deg.)90.000, 113.247, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 43 through 136 or resid 138...
d_2ens_1(chain "C" and (resid 43 through 136 or resid 138...
d_1ens_2(chain "B" and (resid 63 or (resid 64 and (name...
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROHISHISAA43 - 1363 - 96
d_12ens_1THRTHRHISHISAA138 - 25098 - 210
d_21ens_1PROPROHISHISCC43 - 1363 - 96
d_22ens_1THRTHRHISHISCC138 - 25098 - 210
d_11ens_2GLYGLYPROPROBB63 - 1125 - 54
d_21ens_2GLYGLYPROPRODD63 - 1125 - 54

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.687748506915, -0.275613494988, 0.671594515029), (-0.194627830206, -0.961262079008, -0.195179976359), (0.699372575203, 0.00352375408172, -0.714748616096)-6.95293746865, -12.8546823602, 3.13309071759
2given(0.662627697418, -0.279219423044, 0.694953990139), (-0.206001300516, -0.960063900097, -0.189316591761), (0.720061107685, -0.0177150084854, -0.693684495772)-7.19900636346, -13.2434805574, 3.02484268385

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Components

#1: Protein Zwei Ig domain protein zig-4


Mass: 23689.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zig-4 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5ECB1
#2: Protein Probable insulin-like peptide beta-type 5 / INS-6


Mass: 6497.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ins-6 / Cell (production host): Baculovirus / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P56174
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium/potassium phosphate, 0.1 M bis-tris propane, pH 6.8, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→200 Å / Num. obs: 28028 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 56.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.131 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4412 / CC1/2: 0.652 / Rsym value: 1.131 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5015refinement
XDS20190806data reduction
XDS20190806data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→53.13 Å / SU ML: 0.3491 / Cross valid method: FREE R-VALUE / Phase error: 37.3522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1374 4.91 %Random selection
Rwork0.2152 26612 --
obs0.2172 27986 98.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→53.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 0 7 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263948
X-RAY DIFFRACTIONf_angle_d0.63115372
X-RAY DIFFRACTIONf_chiral_restr0.0446621
X-RAY DIFFRACTIONf_plane_restr0.0067701
X-RAY DIFFRACTIONf_dihedral_angle_d15.86391394
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.742136151496
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.06010811591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.47211330.43522584X-RAY DIFFRACTION95.27
2.38-2.470.45131310.38792630X-RAY DIFFRACTION98.89
2.47-2.590.41961250.33722683X-RAY DIFFRACTION99.08
2.59-2.720.36251190.31872660X-RAY DIFFRACTION99.04
2.72-2.890.30881420.28332630X-RAY DIFFRACTION98.58
2.89-3.120.33441310.24362693X-RAY DIFFRACTION99.44
3.12-3.430.27031420.22342656X-RAY DIFFRACTION99.36
3.43-3.930.21511440.19952674X-RAY DIFFRACTION98.6
3.93-4.950.19611330.16012688X-RAY DIFFRACTION98.12
4.95-53.130.21541740.17782714X-RAY DIFFRACTION98.16

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