[English] 日本語
Yorodumi
- PDB-2hfg: Crystal structure of hBR3 bound to CB3s-Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hfg
TitleCrystal structure of hBR3 bound to CB3s-Fab
Components
  • CB3s Fab heavy chain
  • CB3s Fab light chain (kappa)
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsIMMUNE SYSTEM / fab fragment / TNFRSF / antibody-receptor complex / CRD
Function / homology
Function and homology information


B cell costimulation / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell proliferation / positive regulation of B cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / TNFR2 non-canonical NF-kB pathway / signaling receptor activity / adaptive immune response / external side of plasma membrane ...B cell costimulation / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell proliferation / positive regulation of B cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / TNFR2 non-canonical NF-kB pathway / signaling receptor activity / adaptive immune response / external side of plasma membrane / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site ...Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein DKFZp686I04196 / : / Tumor necrosis factor receptor superfamily member 13C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsHymowitz, S.G.
CitationJournal: Blood / Year: 2006
Title: Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells.
Authors: Lee, C.V. / Hymowitz, S.G. / Wallweber, H.J. / Gordon, N.C. / Billeci, K.L. / Tsai, S.P. / Compaan, D.M. / Yin, J. / Gong, Q. / Kelley, R.F. / Deforge, L.E. / Martin, F. / Starovasnik, M.A. / Fuh, G.
History
DepositionJun 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: CB3s Fab light chain (kappa)
H: CB3s Fab heavy chain
R: Tumor necrosis factor receptor superfamily member 13C


Theoretical massNumber of molelcules
Total (without water)52,9883
Polymers52,9883
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-35 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.408, 146.408, 146.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Antibody CB3s Fab light chain (kappa)


Mass: 23250.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Cell line (production host): 4B8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PIH7
#2: Antibody CB3s Fab heavy chain


Mass: 24414.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Cell line (production host): 4B8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N093
#3: Protein Tumor necrosis factor receptor superfamily member 13C / B cell-activating factor receptor / BAFF receptor / BAFF-R / BLyS receptor 3 / CD268 antigen


Mass: 5323.125 Da / Num. of mol.: 1 / Fragment: cysteine rich domain (residues 7-54) / Mutation: V20N, L27P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13C, BAFFR, BR3 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: Q96RJ3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growDetails: Drops contained 2.1 microliters protein solution (pH 6.5) and 2.9 microliters of (0.1M citric acid pH 3.0, 24% PEG 3350, and 0.1 M Praseodymium (III) acetate) over a reservoir of 24% PEG ...Details: Drops contained 2.1 microliters protein solution (pH 6.5) and 2.9 microliters of (0.1M citric acid pH 3.0, 24% PEG 3350, and 0.1 M Praseodymium (III) acetate) over a reservoir of 24% PEG 3350. pH of final drop ~4.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2004
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 16168 / Num. obs: 16168 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.064 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1598 / Rsym value: 0.44 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CB2-Fab

Resolution: 2.61→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 23.633 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 1.455 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25245 1595 10 %RANDOM
Rwork0.19462 ---
all0.20052 15891 --
obs0.20052 15891 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.436 Å2
Refinement stepCycle: LAST / Resolution: 2.61→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 27 3475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223534
X-RAY DIFFRACTIONr_bond_other_d0.0010.023109
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9564819
X-RAY DIFFRACTIONr_angle_other_deg0.75137278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45324.167132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14315547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3461515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02686
X-RAY DIFFRACTIONr_nbd_refined0.2040.2542
X-RAY DIFFRACTIONr_nbd_other0.1860.22882
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21651
X-RAY DIFFRACTIONr_nbtor_other0.0830.22099
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0720.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8072.52917
X-RAY DIFFRACTIONr_mcbond_other0.482.5932
X-RAY DIFFRACTIONr_mcangle_it3.70253704
X-RAY DIFFRACTIONr_scbond_it2.3272.51473
X-RAY DIFFRACTIONr_scangle_it3.44551115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.614→2.668 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.379 94 -
Rwork0.281 838 -
obs--100 %
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)
10.3007-0.2346-0.12922.84081.21471.96010.0890.1206-0.00140.0228-0.23870.210.0495-0.27010.1497-0.10580.04840.05710.02730.0059-0.033752.113639.0426-76.2596
21.14390.3092-1.23562.691-2.93298.1719-0.19190.0216-0.1859-0.08510.15390.09370.749-0.4690.0380.0644-0.14150.1355-0.0225-0.0178-0.032148.56047.3105-57.7793
31.46370.7975-1.35772.7186-1.06172.0569-0.1448-0.0684-0.02960.3580.01780.00460.08520.0160.127-0.00590.06790.0665-0.04390.004-0.079555.590848.2491-56.8941
42.3038-0.8184-1.10663.52891.05513.3854-0.1359-0.1631-0.10540.21890.0856-0.03290.20.18730.05030.00590.03750.1083-0.0410.0468-0.122260.830516.1493-51.3081
54.8982-0.9958-0.74265.38051.73590.879-0.15150.00720.06730.1727-0.0371-0.1221-0.2563-0.22420.1886-0.07520.07710.0249-0.03290.0457-0.164259.160763.1911-71.5687
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1091 - 110
2X-RAY DIFFRACTION2LA110 - 212111 - 213
3X-RAY DIFFRACTION3HB1 - 1141 - 126
4X-RAY DIFFRACTION4HB115 - 214127 - 226
5X-RAY DIFFRACTION5RC13 - 3910 - 36

+
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