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- PDB-8gho: GUCY2C-peptide bound to anti-GUCY2C-scFv antibody -

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Basic information

Entry
Database: PDB / ID: 8gho
TitleGUCY2C-peptide bound to anti-GUCY2C-scFv antibody
Components
  • Guanylyl cyclase C peptide
  • anti-GUCY2C-scFv antibody heavy chain
  • anti-GUCY2C-scFv antibody light chain
KeywordsPROTEIN BINDING / bi-specific antibody GUCY2C antigen
Function / homology
Function and homology information


Intestinal infectious diseases / Digestion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / adenylate cyclase activity / toxic substance binding / response to toxic substance ...Intestinal infectious diseases / Digestion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / adenylate cyclase activity / toxic substance binding / response to toxic substance / regulation of cell population proliferation / protein kinase activity / intracellular signal transduction / GTP binding / endoplasmic reticulum membrane / ATP binding / plasma membrane
Similarity search - Function
Membrane Guanylate Cyclase receptor GC-C, pseudokinase domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Periplasmic binding protein-like I / Protein tyrosine and serine/threonine kinase ...Membrane Guanylate Cyclase receptor GC-C, pseudokinase domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Periplasmic binding protein-like I / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMosyak, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Molecular insights into recognition of GUCY2C by T-cell engaging bispecific antibody anti-GUCY2CxCD3.
Authors: Rampuria, P. / Mosyak, L. / Root, A.R. / Svenson, K. / Agostino, M.J. / LaVallie, E.R.
History
DepositionMar 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-GUCY2C-scFv antibody heavy chain
B: anti-GUCY2C-scFv antibody light chain
C: Guanylyl cyclase C peptide
G: Guanylyl cyclase C peptide
H: anti-GUCY2C-scFv antibody heavy chain
L: anti-GUCY2C-scFv antibody light chain


Theoretical massNumber of molelcules
Total (without water)57,4426
Polymers57,4426
Non-polymers00
Water9,674537
1
A: anti-GUCY2C-scFv antibody heavy chain
B: anti-GUCY2C-scFv antibody light chain
C: Guanylyl cyclase C peptide


Theoretical massNumber of molelcules
Total (without water)28,7213
Polymers28,7213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-18 kcal/mol
Surface area12500 Å2
MethodPISA
2
G: Guanylyl cyclase C peptide
H: anti-GUCY2C-scFv antibody heavy chain
L: anti-GUCY2C-scFv antibody light chain


Theoretical massNumber of molelcules
Total (without water)28,7213
Polymers28,7213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-18 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.680, 80.570, 90.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody anti-GUCY2C-scFv antibody heavy chain


Mass: 13637.258 Da / Num. of mol.: 2 / Fragment: VH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody anti-GUCY2C-scFv antibody light chain


Mass: 13127.521 Da / Num. of mol.: 2 / Fragment: VL domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Guanylyl cyclase C peptide / GC-C / Heat-stable enterotoxin receptor / STA receptor / hSTAR / Intestinal guanylate cyclase


Mass: 1956.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25092, guanylate cyclase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 200 mM Lithium Sulfate, bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→60 Å / Num. obs: 49431 / % possible obs: 92.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.3
Reflection shellResolution: 1.6→1.77 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.9 / Num. unique obs: 2472 / % possible all: 61.7

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Processing

Software
NameClassification
STARANISOdata scaling
BUSTERrefinement
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2528 5.11 %RANDOM
Rwork0.197 ---
obs0.198 49431 71.4 %-
Displacement parametersBiso mean: 32.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.4365 Å20 Å20 Å2
2--1.0133 Å20 Å2
3----1.4498 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 1.6→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 0 537 4460
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084013HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095434HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1356SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes669HARMONIC5
X-RAY DIFFRACTIONt_it4013HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion14.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion521SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4907SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2445 -7.76 %
Rwork0.235 107 -
all0.2358 116 -
obs--2.35 %
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)
11.03130.1525-0.32510.4319-0.31840.93650.01210.0196-0.039-0.0152-0.03980.0066-0.0605-0.00650.0277-0.0151-0.0187-0.0021-0.0038-0.0345-0.0347-27.907372.459627.062
200.1959-0.24020.40990.39092.0853-0.00210.034-0.03120.0688-0.04670.04270.0338-0.00530.0489-0.04380.02190.00940.0119-0.0176-0.0218-36.010367.713948.0485
300.09520.018600.05320-0.0005-0.00080.00080.00060.00050.00240.0033-0.00040-0.012-0.0046-0.02540.0134-0.0348-0.0051-47.492864.269523.9868
40.07750.20060.09460.05630.14680.03880.001-0.00260.00090.0037-0.0012-0.00250.00360.00120.00020.0031-0.0321-0.0156-0.0014-0.0148-0.001519.074295.901942.3393
50.56960.2302-0.04790.32990.1850.9250.0144-0.0408-0.00650.0412-0.0372-0.02740.0565-0.03770.02280.0615-0.10640.0135-0.0030.0007-0.06630.00986.596644.802
60.57910.36240.13480.74620.14070.7630.0090.0462-0.03030.0034-0.0016-0.02040.0158-0.0059-0.0074-0.0087-0.0147-0.0031-0.0117-0.0131-0.01487.088387.259224.2285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ G|* }
5X-RAY DIFFRACTION5{ H|* }
6X-RAY DIFFRACTION6{ L|* }

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