[English] 日本語
Yorodumi
- PDB-8rtx: Crystal Structure of an Anti-idiotype Fab Fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rtx
TitleCrystal Structure of an Anti-idiotype Fab Fragment
Components
  • Anti-IC Fab fragment B12 heavy chain
  • Anti-IC Fab fragment B12 light chain
KeywordsIMMUNE SYSTEM / Fab / idiotype
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEronen, V. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Febs J. / Year: 2024
Title: Structural insights into ternary immunocomplex formation and cross-reactivity: binding of an anti-immunocomplex FabB12 to Fab220-testosterone complex.
Authors: Eronen, V. / Takkinen, K. / Torni, A. / Peng, K. / Janis, J. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J.
History
DepositionJan 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anti-IC Fab fragment B12 light chain
B: Anti-IC Fab fragment B12 heavy chain
C: Anti-IC Fab fragment B12 light chain
D: Anti-IC Fab fragment B12 heavy chain
E: Anti-IC Fab fragment B12 light chain
F: Anti-IC Fab fragment B12 heavy chain


Theoretical massNumber of molelcules
Total (without water)141,1426
Polymers141,1426
Non-polymers00
Water00
1
A: Anti-IC Fab fragment B12 light chain
B: Anti-IC Fab fragment B12 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0472
Polymers47,0472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Anti-IC Fab fragment B12 light chain
D: Anti-IC Fab fragment B12 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0472
Polymers47,0472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Anti-IC Fab fragment B12 light chain
F: Anti-IC Fab fragment B12 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0472
Polymers47,0472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.857, 81.857, 181.927
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_3ens_1chain "E"
d_1ens_2(chain "B" and (resid 1 through 130 or resid 139 through 221))
d_2ens_2(chain "D" and (resid 1 through 130 or resid 139 through 221))
d_3ens_2(chain "F" and (resid 1 through 130 or resid 139 through 221))

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_1ASPASPCYSCYSAA1 - 2141 - 214
d_21ens_1ASPASPCYSCYSCC1 - 2141 - 214
d_31ens_1ASPASPCYSCYSEE1 - 2141 - 214
d_11ens_2GLNGLNALAALABB1 - 1301 - 130
d_12ens_2GLYGLYCYSCYSBB139 - 221139 - 221
d_21ens_2GLNGLNALAALADD1 - 1301 - 130
d_22ens_2GLYGLYCYSCYSDD139 - 221139 - 221
d_31ens_2GLNGLNALAALAFF1 - 1301 - 130
d_32ens_2GLYGLYCYSCYSFF139 - 221139 - 221

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.494077019631, 0.869417944745, 0.000579679773217), (0.86941635097, 0.494074542433, 0.0023569438837), (0.00176276428853, 0.00166849488266, -0.999997054389)-40.7238516191, 23.8772698565, 22.9005469138
2given(-0.559483455022, 0.828281673821, 0.0304586993913), (0.826355736415, 0.554584764362, 0.0978362715554), (0.0641440601397, 0.079907496202, -0.994736312597)-44.7334475142, 68.5457260481, 30.8312198687
3given(-0.506867879556, 0.862022341404, -0.00156063934105), (0.862021430691, 0.506869886136, 0.00140412191621), (0.00200142554692, -0.000633600259259, -0.999997796421)-40.8553682253, 23.3182402743, 22.9204641789
4given(-0.568635449549, 0.821709740926, 0.038037181606), (0.820931028996, 0.563946897964, 0.0896445308349), (0.0522108336338, 0.0822009607268, -0.995247220999)-44.6714053194, 68.2005457466, 29.9670110989

-
Components

#1: Antibody Anti-IC Fab fragment B12 light chain


Mass: 23131.662 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Anti-IC Fab fragment B12 heavy chain


Mass: 23915.613 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium sulfate, imidazole

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.7→40.93 Å / Num. obs: 35497 / % possible obs: 94.6 % / Redundancy: 2.05 % / CC1/2: 0.998 / Net I/σ(I): 9.76
Reflection shellResolution: 2.7→2.77 Å / Num. unique obs: 2632 / CC1/2: 0.616

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.93 Å / Cross valid method: FREE R-VALUE / σ(F): 61.37 / Phase error: 34.7039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 2122 5.98 %
Rwork0.2469 33345 -
obs0.2496 35467 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.69 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 0 0 9738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00989954
X-RAY DIFFRACTIONf_angle_d1.630513527
X-RAY DIFFRACTIONf_chiral_restr0.08871527
X-RAY DIFFRACTIONf_plane_restr0.01151737
X-RAY DIFFRACTIONf_dihedral_angle_d6.14321389
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.96273368157
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.02222184455
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.879640397562
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.884290441093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.45611450.412359X-RAY DIFFRACTION87.6
2.77-2.840.31961400.38492408X-RAY DIFFRACTION89.09
2.84-2.920.29621390.33632408X-RAY DIFFRACTION89.72
2.92-3.020.36511380.32482409X-RAY DIFFRACTION90.33
3.02-3.130.36421410.29912438X-RAY DIFFRACTION91.24
3.13-3.250.30591510.29892435X-RAY DIFFRACTION90.55
3.25-3.40.34141430.28892342X-RAY DIFFRACTION87.78
3.4-3.580.2431520.27652409X-RAY DIFFRACTION89.99
3.58-3.80.31761560.26582345X-RAY DIFFRACTION88.59
3.8-4.10.24741460.25252436X-RAY DIFFRACTION89.79
4.1-4.510.24021380.22132349X-RAY DIFFRACTION88.28
4.51-5.160.21641600.20292400X-RAY DIFFRACTION89.62
5.16-6.490.27491300.22642371X-RAY DIFFRACTION89.07
6.5-40.930.25941410.21612338X-RAY DIFFRACTION86.69
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)
12.52480841649-0.2670424020441.04649380913.954240474970.9437105405352.13197459923-0.9864586813260.215222857909-0.5301300183440.6312154778710.03024377164940.05280608978961.00492316652-1.682283903830.8834745779611.09306964699-0.246698346092-0.07524174943581.093170569140.1096483189610.460147095113-48.760509281923.30561961548.5122653457
22.108383336111.51458966236-0.7331989817811.761921932480.7500324105381.13044120195-0.438258907804-0.373635271740.489160464010.622849162630.229433530107-0.200936935417-0.433904815374-1.778782710870.2219883753431.10344876288-0.117873425624-0.143861982211.549107193520.1080128483930.332400652935-50.187873716732.686306899311.4677308038
31.79337328395-0.297596447643-0.6965142547041.67854689387-0.7792224822370.872338774538-0.1479143132560.1093587041190.0410233388013-0.03851873843730.1452120096530.0693034056421-0.187397768236-0.0427988495065-0.01184132887061.03010161412-0.132447830509-0.1604986364571.112290135420.05177426276850.294660087794-31.722964314423.5354140877-2.62404150944
42.515835133460.2162909331970.6244260092861.22581901808-0.5299818256190.6067242262450.227848271072-0.202489265547-0.1198345765320.075474156135-0.2533551797060.0195312029140.6640283802050.446920758570.005416832316471.36199469207-0.188023433717-0.00459491927111.333010616650.06601536467620.30814766192-26.235611582816.737663131-8.92207735048
57.40494755132-4.59079922213-0.9849977232852.368051600413.819110033627.118486146110.6955128332842.28068516552-0.26205657-0.896564877417-0.3504375963520.739061372010.3484928961080.411704965404-0.2602173743281.129175658410.127045505264-0.1136220418640.852533215521-0.07660999288450.708209599331-26.352416040710.2912811042-17.0030053343
62.356722439020.3329634973651.544829498112.598079494410.2746040920162.84578039354-0.8729957462790.0174161560876-0.586041077638-0.7579323990610.715410375211-0.175463193914-2.019393997870.98310964609-0.06390437539791.630123201320.00527495954954-0.2900834560111.42192318689-0.03347971032320.210534784962-30.321611063139.460285513719.2953487208
76.81799308540.9313635609393.877370660690.4017182704431.538398579925.08620224893-0.5088989853872.288283378860.082461898274-1.03349729012-1.280316230470.168600622314-0.07682986476181.942134836390.9133169550831.25114016647-0.701235462834-0.03612471151171.89522130390.8592482916280.80471648343-20.135862356122.3391697478-22.2438633324
85.670038787240.2424321772062.690251559332.324425249690.04066533296091.208365903860.191638655158-0.01089436541470.08537176309960.0715163165908-0.355080342442-0.2137914022320.931755014491-0.8240842068950.2013129544661.09873487147-0.2493132944320.05476387759121.01391599627-0.02759282306140.497937740897-20.422742574331.8256490499-13.8382186017
90.2324129107740.351642620625-0.2300995232940.427173189879-1.233348545076.449889397780.8838406525160.506869345184-1.33998252654-0.05504384238270.1102590360470.4717265920891.61802287817-0.484297367914-0.7894766941141.58512252201-0.114491788899-0.2862749709311.167578018630.1762505529190.5198521527083.79649937051-6.9374961560114.4328869342
102.97691705353-0.6797154953960.5188933106523.30262896058-2.362850268413.24654090090.0892277337346-0.17584797279-0.366154629219-0.04649565762170.0528156580925-0.06270504082141.229523912670.963254458954-0.1656150477611.291752452470.0990620576488-0.04808727523241.206671241220.03647496212580.3969124412.4678482963-3.6198196845411.3981855437
110.3953898692980.2738058700510.6364611965640.4724651177760.6919491276891.362954313540.1459082613690.168430466353-0.1038811531790.127236830120.05376270454070.178356785885-0.11775453729-0.62284392289-0.2200612090941.17208303112-0.094331842332-0.04294142967241.126887682040.2401267574060.446104757151-4.525203429987.872242864925.5981588732
121.03662464493-0.2662422462220.6668868576121.21388698675-0.3917550498351.827930688290.07820119939530.371408126394-0.14507047502-0.242540665142-0.06054092686810.188144313960.155061714579-0.05394776938890.02395317720361.50269693231-0.147655179508-0.1020829031061.032367159940.01871187986090.35253021615-13.24563676539.3375009575331.722437807
137.05839559865-5.428531409053.253396750098.51536431268-4.264282246323.26207059682-0.432019372075-0.7566028553720.1209313278411.514202800280.42041242740.5694817824310.818740217305-1.205369600120.06345082057082.25883886299-0.27515872766-0.2460501753581.364126722120.1343211252030.0667854184195-18.90697448666.1350154548739.8956191884
140.79967135602-0.07162477134461.013612691730.00666556999594-0.4740925413364.32161540577-0.1130500348810.4054432589170.4866638579810.1492991227230.05798133431770.169981018237-0.6135821463750.4396392530630.0620345228441.45993922664-0.164524712267-0.07759280017241.152443395420.1384039491530.4459458719126.5386118856717.26549795667.60265524662
153.58802444726-1.722251395073.506855336485.06781040919-2.519239063323.654809630790.2173915833430.01875990641540.2639718047450.269435991876-0.226745154925-0.0625245682667-0.294432752977-0.137630319432-0.02654531874281.55947308138-0.2023182386070.02555330092880.949606794096-0.05476928260850.483641276637-3.00982956121.772691122336.6687248469
164.314368830041.22661809695-1.808857099795.990102469510.341314335990.636576673093-0.4903266926960.135199054788-0.296938344055-0.3177360372140.330392248747-0.141432579793-0.03652509846250.2240684933810.1458171099071.058579579870.0923053405374-0.03160271674180.8085478584640.03361777538320.41523767938.6198255619845.100710221819.2642228355
173.15725231980.153598375985-2.371466547520.8330099859291.465096734822.6861039184-0.06698456343550.0436869226542-0.08647580355380.200315474712-0.02272180865860.007501760495410.590037643998-0.2039359488140.1042098941151.14584806032-0.01628797966-0.01002569882210.9421578628690.073669767250.360124384959-13.606030389655.256579337337.3896993425
188.97837936629-4.80716574514-1.261511564398.56331048464-4.501767882477.79383643635-1.08030862668-2.13273744177-0.5292303185232.024131215461.279858088690.5567262544460.777473563933-0.538938005354-0.2355854571751.03912930823-0.0489545608283-0.05650056362971.644197520820.1104468720780.398157628847-22.16227595450.944510143547.3507099594
192.76288659598-0.552310401024-2.389406340460.5772121919371.347845297741.536929866640.1697394142040.1526958150910.291481904929-0.19844106257-0.07154911445-0.177335598986-0.3035509545970.112426424639-0.08454779045861.11719897409-0.039759974147-0.008159434322790.8792044895050.1125499444790.4731969322460.28804718884266.996163585825.6507844364
205.67115662475-4.633239985393.762651476725.709323581391.6450220482.04018460783-1.10460590631-0.399725511507-0.3923614878010.7497588351340.16546925533-0.2073789814291.605842965020.2030005577290.6342798416092.02880640872-0.03184664192890.1056689750791.53255477559-0.3068485067610.163235703185-11.924200680172.478783598350.5495909727
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 25 )AA1 - 251 - 25
22chain 'A' and (resid 26 through 90 )AA26 - 9026 - 90
33chain 'A' and (resid 91 through 128 )AA91 - 12891 - 128
44chain 'A' and (resid 129 through 198 )AA129 - 198129 - 198
55chain 'A' and (resid 199 through 214 )AA199 - 214199 - 214
66chain 'B' and (resid 1 through 124 )BB1 - 1241 - 124
77chain 'B' and (resid 125 through 139 )BB125 - 139125 - 139
88chain 'B' and (resid 140 through 221 )BB140 - 221140 - 221
99chain 'C' and (resid 1 through 25 )CC1 - 251 - 25
1010chain 'C' and (resid 26 through 90 )CC26 - 9026 - 90
1111chain 'C' and (resid 91 through 128 )CC91 - 12891 - 128
1212chain 'C' and (resid 129 through 198 )CC129 - 198129 - 198
1313chain 'C' and (resid 199 through 214 )CC199 - 214199 - 214
1414chain 'D' and (resid 1 through 139 )DD1 - 1391 - 139
1515chain 'D' and (resid 140 through 221 )DD140 - 221140 - 221
1616chain 'E' and (resid 1 through 90 )EE1 - 901 - 90
1717chain 'E' and (resid 91 through 198 )EE91 - 19891 - 198
1818chain 'E' and (resid 199 through 214 )EE199 - 214199 - 214
1919chain 'F' and (resid 1 through 208 )FF1 - 2081 - 208
2020chain 'F' and (resid 209 through 221 )FF209 - 221209 - 221

+
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