[English] 日本語
Yorodumi
- PDB-6hgu: Crystal Structure of an anti-APP-tag Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hgu
TitleCrystal Structure of an anti-APP-tag Fab
Components
  • anti-APP-tag Fab heavy-chain
  • anti-APP-tag Fab light-chain
KeywordsIMMUNE SYSTEM / IgG / Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsRondeau, J.M. / Goepfert, A.
CitationJournal: Immunity / Year: 2020
Title: Structural Analysis Reveals that the Cytokine IL-17F Forms a Homodimeric Complex with Receptor IL-17RC to Drive IL-17RA-Independent Signaling.
Authors: Goepfert, A. / Lehmann, S. / Blank, J. / Kolbinger, F. / Rondeau, J.M.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: anti-APP-tag Fab heavy-chain
B: anti-APP-tag Fab light-chain
H: anti-APP-tag Fab heavy-chain
L: anti-APP-tag Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5749
Polymers95,9674
Non-polymers6075
Water14,628812
1
A: anti-APP-tag Fab heavy-chain
B: anti-APP-tag Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4986
Polymers47,9832
Non-polymers5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-20 kcal/mol
Surface area19510 Å2
MethodPISA
2
H: anti-APP-tag Fab heavy-chain
L: anti-APP-tag Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0763
Polymers47,9832
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-25 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.240, 67.840, 77.860
Angle α, β, γ (deg.)109.760, 92.360, 115.300
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody anti-APP-tag Fab heavy-chain / 6E10A5 Fab


Mass: 23832.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody anti-APP-tag Fab light-chain / anti-APP Fab


Mass: 24150.826 Da / Num. of mol.: 2 / Fragment: anti-APP-tag Fab heavy-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.79 Å3/Da / Density % sol: 55.94 % / Mosaicity: 0.23 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 20% isopropanol, 10% PEG 1,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.5→35.75 Å / Num. obs: 159668 / % possible obs: 96.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Net I/σ(I): 14.3 / Num. measured all: 1150437 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.584.20.525229020.8930.2910.60194.5
4.75-35.7560.02249900.9990.010.02495.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
BUSTER2.11.7refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IFL

3ifl


Resolution: 1.5→15.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.068
RfactorNum. reflection% reflectionSelection details
Rfree0.207 7948 4.98 %RANDOM
Rwork0.187 ---
obs0.188 159563 96.4 %-
Displacement parametersBiso max: 124.33 Å2 / Biso mean: 31.9 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--3.1219 Å23.9687 Å23.9884 Å2
2--4.2976 Å2-2.3678 Å2
3----1.1756 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.5→15.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 39 812 7485
Biso mean--35.71 42.01 -
Num. residues----864
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2258SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1128HARMONIC5
X-RAY DIFFRACTIONt_it6855HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion925SEMIHARMONIC5
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_contact8202SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6855HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9347HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion4.3
X-RAY DIFFRACTIONt_other_torsion13.79
LS refinement shellResolution: 1.5→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2325 549 4.73 %
Rwork0.2258 11054 -
all0.2261 11603 -
obs--93.79 %
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)
11.7478-0.79290.45771.6556-0.35390.8187-0.13890.10070.0164-0.110.0622-0.00740.0124-0.00360.0767-0.0332-0.0175-0.005-0.01960.0002-0.04183.787218.89174.3143
21.50660.01720.79482.18780.08231.5594-0.0786-0.02570.13210.0981-0.0352-0.1631-0.078-0.0130.1138-0.05380.0117-0.0165-0.05250.0111-0.032818.781916.283120.1644
34.71873.9780.30013.99460.13320.5062-0.3170.3713-0.1097-0.40210.3124-0.1001-0.0180.01480.0046-0.0304-0.04170.0159-0.0656-0.0213-0.042715.920153.12043.4197
41.8267-0.39460.08213.08190.45340.85540.081-0.0883-0.02320.459-0.0577-0.20220.1088-0.0715-0.02330.0176-0.0237-0.0256-0.09370.0176-0.03714.249952.620919.3852
50.54390.00960.50190.8054-0.19772.61870.0156-0.06640.0673-0.00540.02390.0656-0.0233-0.1093-0.0395-0.02510.00020.0035-0.02830.0127-0.03831.128936.5924-26.4491
61.37440.03940.43211.8343-0.17231.45870.0245-0.0536-0.02370.0663-0.0239-0.0620.0818-0.0201-0.0006-0.0469-0.0099-0.0231-0.01930.0298-0.062241.713325.6871-10.5203
72.10642.8776-0.6075.7934-1.69620.7757-0.20530.14140.243-0.44570.26570.4715-0.0335-0.0419-0.06030.0568-0.0703-0.0522-0.12950.0399-0.060214.3624.6616-32.0803
81.52780.42991.54181.95840.86454.13-0.05950.2114-0.205-0.12630.0559-0.38780.04460.30940.0036-0.0201-0.04150.0672-0.0703-0.0133-0.023429.5985-1.6357-30.9537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1group10
2X-RAY DIFFRACTION2group20
3X-RAY DIFFRACTION3group30
4X-RAY DIFFRACTION4group40
5X-RAY DIFFRACTION5group50
6X-RAY DIFFRACTION6group60
7X-RAY DIFFRACTION7group70
8X-RAY DIFFRACTION8group80

+
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