[English] 日本語
Yorodumi
- PDB-3skj: Structural And Functional Characterization of an Agonistic Anti-H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3skj
TitleStructural And Functional Characterization of an Agonistic Anti-Human EphA2 Monoclonal Antibody
Components
  • Antibody, heavy chain
  • Antibody, light chain
  • Ephrin type-A receptor 2
KeywordsIMMUNE SYSTEM / Fab / receptor / Ig fold / ephrin receptor / antibody / antigen / extra-cellular
Function / homology
Function and homology information


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / bone remodeling / transmembrane-ephrin receptor activity / post-anal tail morphogenesis / response to growth factor / activation of GTPase activity / regulation of lamellipodium assembly / tight junction / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / ephrin receptor signaling pathway / RAC3 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / negative regulation of angiogenesis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / axon guidance / receptor protein-tyrosine kinase / ruffle membrane / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / virus receptor activity / lamellipodium / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / phosphorylation / focal adhesion / dendrite / cell surface / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. ...Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Jelly Rolls / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOganesyan, V.Y. / Wu, H. / Dall'Acqua, W.F.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and functional characterization of an agonistic anti-human EphA2 monoclonal antibody.
Authors: Peng, L. / Oganesyan, V. / Damschroder, M.M. / Wu, H. / Dall'Acqua, W.F.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3May 31, 2017Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Antibody, light chain
H: Antibody, heavy chain
M: Antibody, light chain
I: Antibody, heavy chain
E: Ephrin type-A receptor 2
F: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)142,9426
Polymers142,9426
Non-polymers00
Water77543
1
L: Antibody, light chain
H: Antibody, heavy chain
E: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)71,4713
Polymers71,4713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-35 kcal/mol
Surface area28080 Å2
MethodPISA
2
M: Antibody, light chain
I: Antibody, heavy chain
F: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)71,4713
Polymers71,4713
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-38 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.940, 120.859, 286.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTwo biological ensembles are presented in the asymmetric unit.

-
Components

#1: Antibody Antibody, light chain /


Mass: 23482.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human)
#2: Antibody Antibody, heavy chain /


Mass: 24420.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human)
#3: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 23568.516 Da / Num. of mol.: 2 / Fragment: unp residues 23-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human)
References: UniProt: P29317, receptor protein-tyrosine kinase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG 4000, 0.1 M sodium acetate, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 10, 2009
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 67446 / Num. obs: 60701 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / SU B: 23.24 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.569 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27131 2278 5 %RANDOM
Rwork0.21592 ---
obs0.21868 43686 94.41 %-
all-48540 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.433 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2---3.52 Å20 Å2
3---5.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8770 0 0 43 8813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228992
X-RAY DIFFRACTIONr_bond_other_d0.0020.026023
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.94812215
X-RAY DIFFRACTIONr_angle_other_deg0.9293.00314669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.47551133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53624.133375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.229151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1521540
X-RAY DIFFRACTIONr_chiral_restr0.0910.21344
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021821
X-RAY DIFFRACTIONr_nbd_refined0.2010.21460
X-RAY DIFFRACTIONr_nbd_other0.2030.25737
X-RAY DIFFRACTIONr_nbtor_refined0.1880.24204
X-RAY DIFFRACTIONr_nbtor_other0.090.25031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8411.57186
X-RAY DIFFRACTIONr_mcbond_other0.1361.52320
X-RAY DIFFRACTIONr_mcangle_it1.0529146
X-RAY DIFFRACTIONr_scbond_it1.72933978
X-RAY DIFFRACTIONr_scangle_it2.4544.53069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.484→2.548 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 127 -
Rwork0.318 2586 -
obs--76.94 %
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)
14.8279-1.65161.7122.87290.02376.11370.14961.14550.244-0.52730.04810.0033-0.06960.0315-0.19760.24610.02920.04430.1869-0.08890.063260.73611.647137.476
23.8989-0.9761.37693.3714-0.21811.9101-0.0506-0.00420.0266-0.14320.04170.0872-0.12810.1050.00880.1235-0.0261-0.00480.1087-0.0349-0.046656.72917.508142.525
36.1074-4.64981.53959.4375-0.9722.8976-0.0312-0.3246-0.0270.61540.16050.27190.0261-0.1295-0.12940.0802-0.0719-0.01060.1583-0.034-0.085959.96513.67151.361
42.31853.0218-1.814211.9229-1.98031.4382-0.30130.84171.4439-0.3144-0.03170.718-0.5668-0.29910.3330.23170.0235-0.06330.26730.0580.236347.2930.361132.716
55.2905-1.7912-0.14033.7403-0.25032.4332-0.00020.39270.4257-0.0594-0.1049-0.5136-0.20460.25540.10510.1114-0.0563-0.00010.1422-0.02940.017664.35817.958143.793
64.20532.64986.008912.11610.147948.9931-1.08090.1441.195-0.25040.19811.03570.5440.05730.88270.269-0.0562-0.26080.32180.12940.310953.20141.72786.334
77.1746-1.75693.46785.6667-2.067612.5951-0.11320.99380.0622-1.10590.07040.22840.130.41030.04280.5616-0.2353-0.22790.4910.18190.147557.59637.91272.155
85.8592-0.76871.363913.2816-7.708311.6844-0.72061.17890.1855-1.6444-0.2397-1.01480.05551.26770.96030.5623-0.26360.02860.54070.080.212367.90336.00975.561
919.957212.31762.725270.4248-37.621757.7908-1.18850.72681.4518-0.8643-0.1377-1.8602-0.17590.581.32610.2987-0.01660.01480.3019-0.00690.301166.02342.73284.728
102.5536-7.42256.860536.0368-7.624928.9216-0.50980.01170.7857-1.2039-0.7732-0.4689-0.4521-0.2491.2830.34-0.1854-0.05510.37910.09880.3158.28443.83377.806
112.83171.07570.36120.67120.12890.4534-0.19110.33460.0156-0.1090.16080.0183-0.0111-0.03720.03040.20170.0003-0.02360.2256-0.0040.023815.17715.161117.335
123.91170.4899-1.16583.0953-2.55486.6559-0.2460.3635-0.1448-0.7631-0.1909-0.28460.36350.41430.43690.3947-0.0861-0.0370.2535-0.0650.020666.18713.92198.623
135.2462-1.07614.90510.71180.50989.26540.7907-0.6983-0.0364-0.0312-0.41360.1605-0.3762-0.283-0.37710.3647-0.0445-0.11640.26020.0760.3159.10121.207100.107
141.78190.38311.23973.093-3.40155.3316-0.07610.11520.07570.07550.0467-0.0955-0.26110.17950.02940.3474-0.0952-0.08950.2201-0.0169-0.018762.98621.10398.722
153.24821.98551.53064.00661.69332.2465-0.14310.3629-0.466-0.35260.20360.08960.20140.0052-0.06050.2961-0.0802-0.04040.4384-0.10940.189548.994-10.62102.616
1618.006512.37156.556520.13329.30819.04470.718-0.0527-1.85130.3044-0.5239-0.17551.04730.1177-0.1940.3098-0.0403-0.07740.298-0.06050.310653.566-16.983105.451
173.77490.1224-1.40672.1269-0.58082.8864-0.00090.049-0.3892-0.08830.0675-0.04180.1720.0741-0.06670.107-0.00680.0040.0836-0.00060.060333.4115.739130.398
184.49741.95341.44911.46440.91380.7928-0.22760.4314-0.4957-0.23490.1588-0.06130.09430.00570.06880.2333-0.03150.03770.2454-0.07660.194918.0471.1117.831
193.80421.93991.88461.21512.2818.6477-0.12960.6301-1.13180.06320.267-0.73710.23140.8993-0.13740.4004-0.05440.21640.3486-0.04110.484110.272-9.58114.73
203.90860.2872.91813.89970.5325.9853-0.07070.5405-0.7215-0.72180.1386-0.24830.3943-0.1277-0.0680.3083-0.08960.1680.3802-0.20950.40966.265-10.849108.629
214.4032.36951.7127.3457-0.48983.2367-0.2870.06290.0068-0.68270.46570.52130.2628-0.492-0.17870.4056-0.2294-0.15660.35170.0472-0.008345.4519.5685.627
220.41721.4042-0.73525.2942-2.31171.3423-0.11840.1633-0.1077-0.23130.42910.30560.0683-0.3173-0.31070.338-0.1586-0.16970.40640.03640.206742.2938.48494.362
233.44282.6796-0.38165.5953-2.47987.9764-0.0765-0.0210.0145-0.00540.04550.4501-0.11560.0760.0310.1921-0.0751-0.10170.3246-0.01020.288435.019-9.563106.462
245.04841.74413.002313.8817-9.088616.2120.17760.3418-0.3618-0.66910.08621.12170.69730.1329-0.26380.3629-0.0921-0.03290.3762-0.02420.347926.735-14.25102.643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 35
2X-RAY DIFFRACTION2E36 - 91
3X-RAY DIFFRACTION3E92 - 125
4X-RAY DIFFRACTION4E126 - 134
5X-RAY DIFFRACTION5E135 - 176
6X-RAY DIFFRACTION6F28 - 43
7X-RAY DIFFRACTION7F44 - 79
8X-RAY DIFFRACTION8F80 - 132
9X-RAY DIFFRACTION9F133 - 142
10X-RAY DIFFRACTION10F163 - 170
11X-RAY DIFFRACTION11H1 - 213
12X-RAY DIFFRACTION12I1 - 38
13X-RAY DIFFRACTION13I39 - 57
14X-RAY DIFFRACTION14I58 - 119
15X-RAY DIFFRACTION15I120 - 213
16X-RAY DIFFRACTION16I215 - 221
17X-RAY DIFFRACTION17L1 - 84
18X-RAY DIFFRACTION18L85 - 129
19X-RAY DIFFRACTION19L130 - 148
20X-RAY DIFFRACTION20L149 - 214
21X-RAY DIFFRACTION21M1 - 84
22X-RAY DIFFRACTION22M85 - 121
23X-RAY DIFFRACTION23M122 - 193
24X-RAY DIFFRACTION24M194 - 214

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more