[English] 日本語
Yorodumi
- PDB-8oi2: Crystal structure of Alb1 megabody in complex with human serum albumin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oi2
TitleCrystal structure of Alb1 megabody in complex with human serum albumin
Components
  • Alb1 Megabody
  • Albumin
KeywordsIMMUNE SYSTEM / nanobody / megabody / albumin
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Helicobacter pylori G27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDe Felice, S. / Zoia, G. / Romanyuk, Z. / Pardon, E. / Steyaert, J. / Angelini, A. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Protein Sci. / Year: 2024
Title: Crystal structure of human serum albumin in complex with megabody reveals unique human and murine cross-reactive binding site.
Authors: De Felice, S. / Romanyuk, Z. / Chinellato, M. / Zoia, G. / Linciano, S. / Kumada, Y. / Pardon, E. / Steyaert, J. / Angelini, A. / Cendron, L.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Albumin
B: Alb1 Megabody


Theoretical massNumber of molelcules
Total (without water)121,0232
Polymers121,0232
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-7 kcal/mol
Surface area48660 Å2
Unit cell
Length a, b, c (Å)370.359, 73.819, 66.130
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Albumin /


Mass: 66214.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Komagataella pastoris (fungus) / References: UniProt: P02768
#2: Antibody Alb1 Megabody


Mass: 54808.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67 % / Description: rod shape
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.03M Sodium fluoride, 0.03M sodium bromide, 0.03M sodium iodide, 0.1M Tris BICINE pH 8.5, 12% v/v ethylene glycol, 6% w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3.25→34.27 Å / Num. obs: 43671 / % possible obs: 98.4 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.044 / Net I/σ(I): 11
Reflection shellResolution: 3.3→3.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4847 / CC1/2: 0.48 / Rpim(I) all: 0.932 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
AutoProcessdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→33.86 Å / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 2177 4.99 %RANDOM
Rwork0.2255 ---
obs0.2279 43671 83.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 0 0 7680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.609
X-RAY DIFFRACTIONf_dihedral_angle_d4.9391038
X-RAY DIFFRACTIONf_chiral_restr0.0381190
X-RAY DIFFRACTIONf_plane_restr0.0051377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.370.46351660.40812483X-RAY DIFFRACTION82
3.37-3.450.40911720.39872620X-RAY DIFFRACTION85
3.45-3.540.38261770.36852557X-RAY DIFFRACTION84
3.54-3.630.38081270.33112687X-RAY DIFFRACTION86
3.63-3.740.35721480.28712632X-RAY DIFFRACTION86
3.74-3.860.35891390.26232739X-RAY DIFFRACTION87
3.86-40.24951230.22752666X-RAY DIFFRACTION86
4-4.160.25711220.22522713X-RAY DIFFRACTION86
4.16-4.350.22621380.20652627X-RAY DIFFRACTION85
4.35-4.570.26711490.19352556X-RAY DIFFRACTION83
4.57-4.860.23531110.17932515X-RAY DIFFRACTION81
4.86-5.230.23791180.21012597X-RAY DIFFRACTION82
5.23-5.760.32151230.25342570X-RAY DIFFRACTION83
5.76-6.580.3293910.28362627X-RAY DIFFRACTION83
6.59-8.270.32761440.24122474X-RAY DIFFRACTION80
8.28-33.860.22451290.18022431X-RAY DIFFRACTION79
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)
16.65391.7707-0.45812.20970.54652.47650.36180.9846-0.4573-0.41610.0010.5437-0.242-1.1776-0.47911.23380.2755-0.20851.7163-0.08851.494426.6725-16.24674.0806
23.743-2.35654.40722.9855-4.22617.3762-0.0698-0.39670.01650.2074-0.0777-0.1034-0.2086-0.00740.18991.2322-0.04920.10531.0731-0.16851.168293.4245-23.087952.0314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 6:583)
2X-RAY DIFFRACTION2(chain B and resseq 1:507)

+
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