[English] 日本語
Yorodumi
- PDB-7eek: Structure of Human serum albumin-Au compound complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eek
TitleStructure of Human serum albumin-Au compound complex
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Delivery / Complex
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
Chem-J2O / PALMITOLEIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, F. / Zhang, J.Z.
CitationJournal: To Be Published
Title: Structure of Human serum albumin-Au compound complex
Authors: Yang, F. / Zhang, J.Z.
History
DepositionMar 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,54916
Polymers132,6862
Non-polymers3,86314
Water00
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2758
Polymers66,3431
Non-polymers1,9327
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2758
Polymers66,3431
Non-polymers1,9327
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.187, 92.207, 95.435
Angle α, β, γ (deg.)105.210, 89.680, 100.100
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Serum albumin


Mass: 66342.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia kudriavzevii (yeast) / References: UniProt: P02768
#2: Chemical
ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-J2O / 11-methyl-2-oxa-4-thia-6,7-diaza-3$l^{3}-auratricyclo[7.4.0.0^{3,7}]trideca-1(13),5,9,11-tetraen-5-amine


Mass: 405.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10AuN3OS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, MPD, DMSO

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36829 / % possible obs: 96.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.088 / Rrim(I) all: 0.155 / Χ2: 0.877 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5420.22617880.2790.3050.4810.7683.6
2.54-2.592.10.36516880.6210.2850.4660.98479.5
2.59-2.642.10.34916160.6650.2730.4460.90775.5
2.64-2.692.20.34915670.6640.2650.4410.94472.6
2.69-2.752.40.32619030.830.2420.4080.92686.8
2.75-2.822.40.31319110.8440.230.390.88189.6
2.82-2.892.50.30319630.870.220.3760.95491.3
2.89-2.962.60.28519480.8990.2040.3520.95789.8
2.96-3.052.60.25619310.9030.1820.3150.91390.7
3.05-3.152.70.23219510.90.1640.2850.96889.7
3.15-3.262.70.218870.9120.1410.2460.95488.6
3.26-3.392.70.16719230.9240.1190.2060.92388.3
3.39-3.552.70.14818360.9450.1040.1820.95684.6
3.55-3.732.80.13317650.9520.0920.1630.95282.3
3.73-3.972.80.12115550.950.0860.1490.95572.4
3.97-4.272.80.10219230.9680.0710.1250.85888.1
4.27-4.72.90.09619430.9730.0650.1170.83990.8
4.7-5.383.10.09119710.9750.060.1090.7691.2
5.38-6.783.20.08718990.9780.0560.1040.61988.2
6.78-503.30.10218610.970.0660.1220.76486.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv1.1refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ5

1bj5


Resolution: 2.5→46.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rwork0.2381 --
obs-34352 97.6 %
Displacement parametersBiso max: 196.94 Å2 / Biso mean: 35.8799 Å2 / Biso min: 14.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9270 0 232 0 9502

+
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://pdbjlc1.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