[English] 日本語
Yorodumi
- PDB-8j7e: Crystal structure of BRIL in complex with 1b3 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j7e
TitleCrystal structure of BRIL in complex with 1b3 Fab
Components
  • Antibody 1b3 Fab Heavy chain
  • Antibody 1b3 Fab Light chain
  • Soluble cytochrome b562
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhong, Y.X. / Guo, Q. / Tao, Y.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0902700 China
CitationJournal: Nat Chem Biol / Year: 2024
Title: A method for structure determination of GPCRs in various states.
Authors: Qiong Guo / Binbin He / Yixuan Zhong / Haizhan Jiao / Yinhang Ren / Qinggong Wang / Qiangqiang Ge / Yongxiang Gao / Xiangyu Liu / Yang Du / Hongli Hu / Yuyong Tao /
Abstract: G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by ...G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by various ligands has been one of the primary goals in the field. Here we developed an effective universal method for GPCR cryo-electron microscopy structure determination without the need to prepare GPCR-signaling protein complexes. Using this method, we successfully solved the structures of the β-adrenergic receptor (βAR) bound to antagonistic and agonistic ligands and the adhesion GPCR ADGRL3 in the apo state. For βAR, an intermediate state stabilized by the partial agonist was captured. For ADGRL3, the structure revealed that inactive ADGRL3 adopts a compact fold and that large unusual conformational changes on both the extracellular and intracellular sides are required for activation of adhesion GPCRs. We anticipate that this method will open a new avenue for understanding GPCR structure‒function relationships and drug development.
History
DepositionApr 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antibody 1b3 Fab Heavy chain
B: Antibody 1b3 Fab Light chain
C: Antibody 1b3 Fab Heavy chain
D: Antibody 1b3 Fab Light chain
E: Soluble cytochrome b562
F: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)125,1426
Polymers125,1426
Non-polymers00
Water3,153175
1
A: Antibody 1b3 Fab Heavy chain
B: Antibody 1b3 Fab Light chain
F: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)62,5713
Polymers62,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-44 kcal/mol
Surface area23930 Å2
MethodPISA
2
C: Antibody 1b3 Fab Heavy chain
D: Antibody 1b3 Fab Light chain
E: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)62,5713
Polymers62,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-41 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.319, 116.319, 212.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Antibody Antibody 1b3 Fab Heavy chain


Mass: 25211.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Antibody 1b3 Fab Light chain


Mass: 25574.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11785.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 295.15 K / Method: liquid diffusion / Details: 0.1 M sodium acetate pH 5.0, 15% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→49.01 Å / Num. obs: 41670 / % possible obs: 99.86 % / Redundancy: 20 % / Biso Wilson estimate: 59.5 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 11.32
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 1.546 / Num. unique obs: 4117 / CC1/2: 0.768 / Rpim(I) all: 0.3516

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.01 Å / SU ML: 0.4267 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2505 2151 5.17 %
Rwork0.1995 39476 -
obs0.2022 41627 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8200 0 0 175 8375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00628392
X-RAY DIFFRACTIONf_angle_d0.811811418
X-RAY DIFFRACTIONf_chiral_restr0.05091278
X-RAY DIFFRACTIONf_plane_restr0.00621458
X-RAY DIFFRACTIONf_dihedral_angle_d17.09313008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.37921440.382615X-RAY DIFFRACTION99.96
2.87-2.940.40441430.31932552X-RAY DIFFRACTION99.96
2.94-3.020.38171340.29472632X-RAY DIFFRACTION99.96
3.02-3.110.31781310.27732609X-RAY DIFFRACTION99.96
3.11-3.210.31841200.25332599X-RAY DIFFRACTION100
3.21-3.320.32941500.25062632X-RAY DIFFRACTION99.93
3.32-3.450.30371330.26292584X-RAY DIFFRACTION99.96
3.45-3.610.2421240.20642633X-RAY DIFFRACTION99.96
3.61-3.80.26731270.19942640X-RAY DIFFRACTION99.96
3.8-4.040.23361590.17972610X-RAY DIFFRACTION100
4.04-4.350.23661470.16822615X-RAY DIFFRACTION100
4.35-4.790.20831570.14642647X-RAY DIFFRACTION100
4.79-5.480.19841370.15552673X-RAY DIFFRACTION100
5.48-6.90.2041900.18972650X-RAY DIFFRACTION99.93
6.9-49.010.22131550.16142785X-RAY DIFFRACTION98.79

+
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