8YLX | pdb_00008ylx

Single particle cryo-EM reconstruction of Oryza sativa recombinant human serum albumin

PDB DOI: https://doi.org/10.2210/pdb8YLX/pdb
EM Map EMD-39392: EMDB EMDataResource

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Oryza sativa
Mutation(s): No

Deposited: 2024-03-07 Released: 2025-03-19
Deposition Author(s): Dong, C.J., Yang, D.C., Duan, B.R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8YLX

This is version 1.0 of the entry. See complete history.

Literature

Single particle cryo-EM reconstruction of Oryza sativa recombinant human serum albumin

Dong, C.J., Yang, D.C., Duan, B.R.

To be published.

Macromolecule Content

Total Structure Weight: 67 kDa
Atom Count: 4,660
Modeled Residue Count: 582
Deposited Residue Count: 585
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Albumin	A	585	Homo sapiens	Mutation(s): 0 Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768 Go to UniProtKB: P02768
PHAROS: P02768 GTEx: ENSG00000163631
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02768
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OCA Query on OCA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32250710142

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.