[English] 日本語
Yorodumi
- PDB-6osh: Potent and Selective Antitumor Antibody Targeting a Membrane-Prox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6osh
TitlePotent and Selective Antitumor Antibody Targeting a Membrane-Proximal Epitope of ROR2
Components
  • Antibody Light chain variable region
  • Antibody heavy chain variable region
  • Tyrosine-protein kinase transmembrane receptor ROR2
KeywordsIMMUNE SYSTEM / Single chain Fv / ScFv / Antibody / ROR2 / Kringle domain / receptor tyrosine kinase-like orphan receptor / Phage display
Function / homology
Function and homology information


WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt-protein binding / PCP/CE pathway / mitogen-activated protein kinase kinase kinase binding / coreceptor activity / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / clathrin-coated endocytic vesicle membrane / receptor protein-tyrosine kinase / Wnt signaling pathway ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt-protein binding / PCP/CE pathway / mitogen-activated protein kinase kinase kinase binding / coreceptor activity / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / clathrin-coated endocytic vesicle membrane / receptor protein-tyrosine kinase / Wnt signaling pathway / receptor complex / positive regulation of cell migration / axon / signal transduction / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, receptor ROR / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site ...Tyrosine-protein kinase, receptor ROR / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Kringle-like fold / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase transmembrane receptor ROR2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.117 Å
AuthorsPark, H. / Rader, C.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Affinity maturation, humanization, and co-crystallization of a rabbit anti-human ROR2 monoclonal antibody for therapeutic applications.
Authors: Goydel, R.S. / Weber, J. / Peng, H. / Qi, J. / Soden, J. / Freeth, J. / Park, H. / Rader, C.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Antibody Light chain variable region
K: Tyrosine-protein kinase transmembrane receptor ROR2
H: Antibody heavy chain variable region


Theoretical massNumber of molelcules
Total (without water)35,0193
Polymers35,0193
Non-polymers00
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-12 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.165, 67.201, 89.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Antibody Light chain variable region


Mass: 11957.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#2: Protein Tyrosine-protein kinase transmembrane receptor ROR2 / Neurotrophic tyrosine kinase / receptor-related 2


Mass: 10688.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROR2, NTRKR2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q01974, receptor protein-tyrosine kinase
#3: Antibody Antibody heavy chain variable region


Mass: 12372.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na citrate tribasic 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.117→40.33 Å / Num. obs: 81433 / % possible obs: 89 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04451 / Rpim(I) all: 0.02156 / Rrim(I) all: 0.04969 / Net I/σ(I): 17.3
Reflection shellResolution: 1.117→1.157 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 4074 / CC1/2: 0.53 / Rpim(I) all: 0.5024 / Rrim(I) all: 0.7565

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BA5

6ba5


Resolution: 1.117→40.332 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 1221 1.5 %
Rwork0.1621 --
obs0.1622 81417 76.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.117→40.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 0 426 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082449
X-RAY DIFFRACTIONf_angle_d0.9833337
X-RAY DIFFRACTIONf_dihedral_angle_d3.0671384
X-RAY DIFFRACTIONf_chiral_restr0.081363
X-RAY DIFFRACTIONf_plane_restr0.007430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.117-1.16170.3197230.28971562X-RAY DIFFRACTION14
1.1617-1.21460.232700.24844603X-RAY DIFFRACTION40
1.2146-1.27870.23151190.22397735X-RAY DIFFRACTION67
1.2787-1.35880.22211670.202710977X-RAY DIFFRACTION95
1.3588-1.46370.19061760.182811558X-RAY DIFFRACTION100
1.4637-1.6110.18251760.163311608X-RAY DIFFRACTION100
1.611-1.84410.1741770.153511603X-RAY DIFFRACTION100
1.8441-2.32330.15331420.14969329X-RAY DIFFRACTION79
2.3233-40.35810.1471710.146511221X-RAY DIFFRACTION93
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)
13.7498-2.2116-2.45432.57073.2284.1053-0.3796-0.3676-0.03610.97850.3024-0.30250.27390.45740.09590.1540.0222-0.03060.17670.00240.134629.1536-2.89313.1623
23.82850.33420.34230.7197-0.57450.5584-0.1593-0.75190.45180.97030.3958-0.31090.08360.3870.04140.2905-0.1299-0.03780.2142-0.02540.262126.754512.31772.5524
31.1562-0.5887-0.69372.7062.29142.14490.08050.07540.5375-0.1472-0.0820.0648-0.74680.0767-0.04050.2956-0.02780.00330.11230.00090.248920.830918.3489-3.1329
41.9585-1.1013-0.67422.55620.3960.90230.01020.00270.04490.0774-0.0368-0.1334-0.02790.06440.01490.0639-0.0077-0.00130.07130.00410.065324.1056-1.6292-2.7057
51.150.5122-0.01221.2032-0.22391.8773-0.01350.0655-0.02860.0485-0.0130.1157-0.0949-0.04880.00670.0585-0.00890.00260.06030.00760.061214.61470.8489-7.2515
62.2424-0.31830.37792.1224-0.02842.3824-0.03680.11770.1637-0.03280.0252-0.1602-0.15670.16320.0040.0739-0.02880.00740.08840.01770.07823.29285.7062-9.949
71.2605-0.3384-0.31342.45450.68391.490.06290.0390.10530.0088-0.0685-0.0026-0.1504-0.04040.02120.07740.00740.00840.0764-0.00060.064816.89383.5916-0.7324
81.6294-0.5316-0.03666.1853-0.12921.550.0615-0.05160.12170.1228-0.0941-0.0822-0.09610.02990.02660.0632-0.01410.00290.0761-0.00750.065420.45823.78534.241
93.4361-0.51482.02091.65890.07341.8765-0.34090.19760.0146-0.09850.01430.14450.0001-0.0475-0.51350.3777-0.1984-0.01290.4594-0.17750.37230.8453-26.5456-28.5363
102.5548-0.31620.15381.8619-0.542.1648-0.10730.1999-0.3133-0.0229-0.02190.13370.3586-0.29290.0850.1321-0.0367-0.00630.136-0.02930.13997.0695-20.7067-25.8129
111.112-0.4358-1.05631.09670.68793.39990.0547-0.0699-0.14610.0468-0.0077-0.04090.27840.0738-0.04870.0806-0-0.02520.08250.00590.082211.4153-17.3016-13.7673
123.6008-0.32240.1460.88760.22192.90130.0088-0.00690.0593-0.0204-0.0107-0.06350.0549-0.1313-0.01150.0947-0.02590.00310.1131-0.00280.11545.2737-17.7901-20.6707
134.31851.2756-0.45372.98811.23543.3198-0.11870.1579-0.0501-0.12990.18070.01990.06750.0763-0.02550.0716-0.0135-0.0040.0863-0.0040.05910.4016-13.8688-23.2709
141.99440.62491.24751.6324-0.65251.538-0.07210.20250.1903-0.11450.0833-0.1003-0.39240.46890.06180.1156-0.04950.01860.152-0.02240.096416.5633-6.6764-22.0575
157.9616.674-0.47358.0077-0.46619.0562-0.1290.27870.0961-0.36330.31010.0196-0.0713-0.22150.07720.0923-0.01060.0080.12110.00820.09679.0006-13.2436-26.576
161.1676-0.3009-0.0870.2283-0.18360.2897-0.11870.284-0.1528-0.08460.2905-0.0289-0.33140.04520.04840.5663-0.24890.23710.4966-0.12550.41182.6176-23.9117-32.3178
176.57832.5973-1.14665.2202-2.09438.6703-0.09210.13520.57380.2401-0.09180.1971-0.6876-0.11560.24070.13270.0179-0.0030.13680.03970.20651.24170.684-5.5546
180.46350.0307-0.02041.388-1.81314.60470.0737-0.06820.07620.04110.02760.0321-0.1128-0.1094-0.09740.0908-0.00760.02640.1102-0.00350.08780.9576-7.417514.497
192.4540.3554-0.00870.75760.20822.31940.00160.1260.0414-0.0080.01030.0765-0.0403-0.07110.0110.05-0.00730.00970.04970.0120.05985.3939-9.1271.3597
202.64911.31320.11971.7899-0.17540.40030.165-0.31780.21560.3278-0.2090.119-0.01420.0335-0.03030.084-0.03290.00680.1132-0.01920.075715.5667-7.40868.7798
210.7873-0.1967-1.03071.142-0.02471.7603-0.0015-0.3255-0.0477-0.00370.019-0.03660.0520.1189-0.01630.0580.0047-0.00450.1011-0.00710.07129.0381-16.72418.5755
224.68661.28114.59070.74851.24374.49920.0549-0.07190.0160.0252-0.04410.0058-0.0061-0.1319-0.00070.06010.0010.00630.0872-0.01620.07184.4438-13.500213.0073
230.35280.1572-0.08450.10290.36514.92810.0738-0.02070.05280.04110.01750.0436-0.10230.1061-0.03680.0826-0.01420.00970.0743-0.00150.07957.8256-5.82333.44
240.27140.1193-0.35780.1759-0.85094.64460.1556-0.09120.05950.13530.00860.0398-0.401-0.0206-0.0410.1256-0.02070.02340.0947-0.00790.08285.6824-2.449912.296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 0:5)
2X-RAY DIFFRACTION2(chain H and resid 6:9)
3X-RAY DIFFRACTION3(chain H and resid 10:19)
4X-RAY DIFFRACTION4(chain H and resid 20:40)
5X-RAY DIFFRACTION5(chain H and resid 41:62)
6X-RAY DIFFRACTION6(chain H and resid 63:82)
7X-RAY DIFFRACTION7(chain H and resid 83:100)
8X-RAY DIFFRACTION8(chain H and resid 101:113)
9X-RAY DIFFRACTION9(chain K and resid 314:318)
10X-RAY DIFFRACTION10(chain K and resid 319:335)
11X-RAY DIFFRACTION11(chain K and resid 336:362)
12X-RAY DIFFRACTION12(chain K and resid 363:372)
13X-RAY DIFFRACTION13(chain K and resid 373:381)
14X-RAY DIFFRACTION14(chain K and resid 382:385)
15X-RAY DIFFRACTION15(chain K and resid 386:389)
16X-RAY DIFFRACTION16(chain K and resid 390:394)
17X-RAY DIFFRACTION17(chain L and resid -2:3)
18X-RAY DIFFRACTION18(chain L and resid 4:23)
19X-RAY DIFFRACTION19(chain L and resid 24:38)
20X-RAY DIFFRACTION20(chain L and resid 39:51)
21X-RAY DIFFRACTION21(chain L and resid 52:69)
22X-RAY DIFFRACTION22(chain L and resid 70:79)
23X-RAY DIFFRACTION23(chain L and resid 80:98)
24X-RAY DIFFRACTION24(chain L and resid 99:110)

+
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