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- PDB-6cxy: Crystal Structure of Human E-cadherin bound by mouse monoclonal a... -

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Basic information

Entry
Database: PDB / ID: 6cxy
TitleCrystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11
Components
  • Cadherin-1
  • Heavy chain
  • Light Chain
KeywordsCELL ADHESION / SSGCID / Cadherin-1 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / flotillin complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / Formation of definitive endoderm / catenin complex / Apoptotic cleavage of cell adhesion proteins / adherens junction organization / GTPase activating protein binding / cell-cell junction assembly / Adherens junctions interactions / ankyrin binding / negative regulation of cell-cell adhesion / apical junction complex / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / Integrin cell surface interactions / RHO GTPases activate IQGAPs / synapse assembly / cell adhesion molecule binding / positive regulation of protein localization / Degradation of the extracellular matrix / Transcriptional and post-translational regulation of MITF-M expression and activity / InlA-mediated entry of Listeria monocytogenes into host cells / protein tyrosine kinase binding / negative regulation of cell migration / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell morphogenesis / beta-catenin binding / cell-cell adhesion / cytoplasmic side of plasma membrane / positive regulation of protein import into nucleus / response to toxic substance / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / neuron projection development / cell junction / cell migration / lamellipodium / actin cytoskeleton / regulation of gene expression / postsynapse / endosome / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11
Authors: Dranow, D.M. / Phan, J.N. / Maker, A.Y. / Schecterson, L.C. / Mangio, R.S. / Gumbiner, B.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cadherin-1
H: Heavy chain
L: Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,73225
Polymers72,3003
Non-polymers1,43222
Water11,494638
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint10 kcal/mol
Surface area29910 Å2
Unit cell
Length a, b, c (Å)122.680, 77.470, 110.940
Angle α, β, γ (deg.)90.000, 92.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-694-

HOH

21C-751-

HOH

31H-457-

HOH

41H-571-

HOH

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Cadherin-1 / CAM 120/80 / Epithelial cadherin / E-cadherin / Uvomorulin


Mass: 23595.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH1, CDHE, UVO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12830

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain


Mass: 24385.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighg1 / Plasmid: pcDNA3.4 / Cell line (production host): Expi-293F / Production host: Homo sapiens (human)
#3: Antibody Light Chain


Mass: 24319.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LC / Plasmid: pcDNA3.4 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 660 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HosaA.19747.a.KW2.PC00156 at 10.3 mg/ml in a buffer containing 50 mM Tris, pH = 8, 150 mM NaCl, and 3 mM CaCl2 was mixed 0.1 uL + 0.1 uL with Wizard 3/4 (h12): 15% (w/v) PEG-20,000, 0.1 M ...Details: HosaA.19747.a.KW2.PC00156 at 10.3 mg/ml in a buffer containing 50 mM Tris, pH = 8, 150 mM NaCl, and 3 mM CaCl2 was mixed 0.1 uL + 0.1 uL with Wizard 3/4 (h12): 15% (w/v) PEG-20,000, 0.1 M HEPES/ NaOH, pH = 7.0. The crystal was cryoprotected with 20% ethylene glycol. Tray: 299140h12, puck: qxp2-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→40.091 Å / Num. obs: 52838 / % possible obs: 99.9 % / Redundancy: 4.19 % / Biso Wilson estimate: 31.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.094 / Χ2: 1.03 / Net I/σ(I): 13.4 / Num. measured all: 221388 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.264.2460.5872.616425387138680.7840.67299.9
2.26-2.324.2530.5113.0216093378637840.830.58499.9
2.32-2.394.2470.4193.6115557366536630.8690.4899.9
2.39-2.464.2540.3714.1115307360035980.8910.42499.9
2.46-2.544.2510.3114.8914722346034630.9230.356100
2.54-2.634.2620.2516.0314334336933630.9510.28799.8
2.63-2.734.2550.1997.5113812324732460.9690.227100
2.73-2.844.2340.169.2413282313931370.9780.18399.9
2.84-2.974.230.12211.8612602298029790.9870.14100
2.97-3.114.1980.10113.9212112288628850.990.116100
3.11-3.284.1670.07917.2911530276827670.9940.091100
3.28-3.484.1140.06420.5210594257525750.9960.073100
3.48-3.724.0750.05224.349817241124090.9970.0699.9
3.72-4.024.0550.04726.249237227822780.9970.054100
4.02-4.44.0460.0429.258367207020680.9980.04699.9
4.4-4.924.0930.03531.457772190018990.9980.0499.9
4.92-5.684.110.03530.826941169116890.9990.0499.9
5.68-6.964.140.036295937143514340.9990.04199.9
6.96-9.844.1070.02932.924542110711060.9990.03399.9
9.84-40.0913.8360.02536.4424056406270.9990.02998

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å40.09 Å
Translation2.2 Å40.09 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o72, 4web

2o72

4web


Resolution: 2.2→40.091 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2648 5.01 %Random selection
Rwork0.1626 50185 --
obs0.1644 52833 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.39 Å2 / Biso mean: 36.399 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 2.2→40.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4849 0 90 646 5585
Biso mean--58.25 43.61 -
Num. residues----640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1999-2.23990.31021430.23725862729
2.2399-2.28290.27031250.222526632788
2.2829-2.32950.2781230.202926312754
2.3295-2.38020.23581310.198126242755
2.3802-2.43550.26781400.191926222762
2.4355-2.49640.26541420.196626532795
2.4964-2.56390.23111130.196326272740
2.5639-2.63940.23621320.180626392771
2.6394-2.72450.22551330.179326292762
2.7245-2.82190.23471440.178526352779
2.8219-2.93480.24281310.174626592790
2.9348-3.06840.22371680.19126152783
3.0684-3.23010.24561640.180526222786
3.2301-3.43230.24081330.176526432776
3.4323-3.69720.1791300.16126452775
3.6972-4.06890.17911270.148126882815
4.0689-4.65690.13671920.113425892781
4.6569-5.86430.1221410.113626812822
5.8643-40.09780.14661360.143927342870
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)
10.39410.17110.31071.27221.38862.4864-0.02160.0661-0.03270.11460.0375-0.0085-0.0355-0.025-0.03150.24780.0111-0.00650.2410.02870.2026-3.0961-3.502348.9508
24.0863-1.2354-1.3413.39830.78165.83660.09340.33880.0209-0.0481-0.0510.1989-0.1698-0.4139-0.03350.16770.0021-0.05020.2112-0.00370.1595-8.29760.901941.7784
33.4358-3.2011-0.79635.28110.9871.9416-0.0558-0.00330.28990.01680.1201-0.3877-0.03470.0516-0.06860.2067-0.0013-0.02240.23770.01410.1787-0.811.884942.4139
49.5065-2.5263-6.07791.73091.19385.1957-0.00510.6061-0.28160.0173-0.17650.19270.082-0.46020.14680.27350.0329-0.06530.3097-0.01740.292120.6598-18.481533.9689
57.4775-2.8438-0.53422.19550.1870.5620.04890.1196-0.0637-0.1142-0.04680.02350.17480.0815-0.00860.26330.0378-0.02650.22620.01780.18636.5926-25.469634.6459
62.3514-2.75131.1765.01730.34962.24860.3061.3445-0.0551-0.3686-0.321-0.35630.23990.1243-0.04790.33390.1146-0.04720.3784-0.00120.170638.5341-25.916226.7251
73.1958-2.4217-2.7732.59373.40964.90450.025-0.06640.5929-0.66630.2466-0.8649-0.22810.3973-0.12570.3146-0.0036-0.02230.3184-0.06990.3839-1.883-27.572815.5321
82.062-0.16240.18734.20971.87452.0049-0.01510.169-0.0483-0.05440.107-0.2985-0.08120.2019-0.09540.3024-0.02190.02150.295-0.040.2728-1.7167-22.537226.6253
92.8436-1.0593-0.27036.4823.11414.20180.02310.1548-0.0476-0.11430.0854-0.3325-0.18350.3243-0.08510.2619-0.00810.0080.3323-0.01740.2183-0.3964-27.126621.0304
101.2361-0.4345-0.55025.87245.26115.27750.0221-0.1122-0.06610.1575-0.17720.0935-0.3091-0.18030.21870.27380.0249-0.03940.2669-0.00950.2015-12.0697-16.632630.7305
110.58321.20930.08744.90913.90365.879-0.04290.09060.04790.10240.0935-0.10610.01380.1036-0.02260.23980.03740.02040.2372-0.02380.2994-3.3183-36.906210.3484
128.0177-4.1823-3.00585.90571.42064.6970.23491.0633-0.7668-0.4394-0.08390.2465-0.0626-0.3612-0.1570.3651-0.0195-0.02780.2420.05490.2455-22.3915-42.6426-1.1119
134.3104-3.97233.68474.8631-1.9895.2329-0.0469-0.3930.8767-0.09980.1587-0.3303-0.167-0.0886-0.10910.3467-0.0020.02120.24140.00480.3123-15.4246-34.69254.5985
145.5811-0.12373.15593.1941-1.76426.31430.1678-0.0295-0.3199-0.1262-0.00130.20480.05780.1124-0.13660.2723-0.04290.02620.2023-0.00350.2345-19.7891-41.10516.4183
152.4537-2.46672.32463.7083-0.80294.27740.18540.78620.4616-0.5293-0.11620.20750.14210.00760.0160.473-0.0185-0.01050.34210.06460.3575-19.665-35.335-4.4487
164.53882.50692.87832.79940.61973.59120.45-0.2261-0.19150.6199-0.40810.13360.6889-0.30860.03530.4486-0.07980.12450.3383-0.04580.3453-22.059-35.695737.626
172.99681.45141.28093.09722.03823.3270.0583-0.15570.01050.235-0.30960.34090.282-0.26070.27950.2548-0.03180.06040.281-0.0470.2516-19.7938-23.99837.0402
184.83151.36211.11943.01522.59314.32030.0240.0684-0.1412-0.0335-0.41210.34550.0019-0.35910.39580.27480.00590.03360.2758-0.04690.2892-24.1774-31.023430.1801
190.99561.08330.85351.86171.34771.3817-0.0225-0.043-0.0661-0.01980.0149-0.04980.03270.0388-0.06810.2889-0.00090.03790.20760.01460.2431-20.0591-39.726617.9788
201.47690.0358-0.44343.14642.1143.21370.04630.0899-0.21910.05290.05210.08450.2633-0.0481-0.05890.3403-0.029-0.00110.28630.00140.3089-27.311-52.19799.2657
213.63341.17660.193.98292.5114.58110.0294-0.1253-0.09490.47910.088-0.19070.30420.1924-0.20040.36510.01340.02430.25880.06480.2299-24.8571-50.318811.9678
228.24290.6384-2.12132.16353.84279.0167-0.2180.3578-0.53050.27230.3988-0.46360.88350.72840.00240.51270.02660.06420.2489-0.00430.3664-18.1029-57.2958-2.0582
234.5031-1.1294-3.94693.23331.66476.6876-0.4240.5517-0.48640.0601-0.12570.32020.7854-0.66980.60040.3582-0.12150.00240.3027-0.04780.3284-32.1325-57.29313.6862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 30 )C1 - 30
2X-RAY DIFFRACTION2chain 'C' and (resid 31 through 62 )C31 - 62
3X-RAY DIFFRACTION3chain 'C' and (resid 63 through 99 )C63 - 99
4X-RAY DIFFRACTION4chain 'C' and (resid 100 through 111 )C100 - 111
5X-RAY DIFFRACTION5chain 'C' and (resid 112 through 201 )C112 - 201
6X-RAY DIFFRACTION6chain 'C' and (resid 202 through 213 )C202 - 213
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 17 )H1 - 17
8X-RAY DIFFRACTION8chain 'H' and (resid 18 through 72 )H18 - 72
9X-RAY DIFFRACTION9chain 'H' and (resid 73 through 98 )H73 - 98
10X-RAY DIFFRACTION10chain 'H' and (resid 99 through 109 )H99 - 109
11X-RAY DIFFRACTION11chain 'H' and (resid 110 through 125 )H110 - 125
12X-RAY DIFFRACTION12chain 'H' and (resid 126 through 151 )H126 - 151
13X-RAY DIFFRACTION13chain 'H' and (resid 152 through 163 )H152 - 163
14X-RAY DIFFRACTION14chain 'H' and (resid 164 through 190 )H164 - 190
15X-RAY DIFFRACTION15chain 'H' and (resid 191 through 219 )H191 - 219
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 25 )L1 - 25
17X-RAY DIFFRACTION17chain 'L' and (resid 26 through 81 )L26 - 81
18X-RAY DIFFRACTION18chain 'L' and (resid 82 through 96 )L82 - 96
19X-RAY DIFFRACTION19chain 'L' and (resid 97 through 134 )L97 - 134
20X-RAY DIFFRACTION20chain 'L' and (resid 135 through 156 )L135 - 156
21X-RAY DIFFRACTION21chain 'L' and (resid 157 through 180 )L157 - 180
22X-RAY DIFFRACTION22chain 'L' and (resid 181 through 194 )L181 - 194
23X-RAY DIFFRACTION23chain 'L' and (resid 195 through 217 )L195 - 217

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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