8Y77 | pdb_00008y77

Crystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains

• PDB DOI: https://doi.org/10.2210/pdb8Y77/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-04 Released: 2025-02-12 
• Deposition Author(s): Cao, Y., Wang, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains

Cao, Y., Wang, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.7 kDa 
• Atom Count: 1,262 
• Modeled Residue Count: 137 
• Deposited Residue Count: 139 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sterile alpha motif domain-containing protein 1	A	66	Homo sapiens	Mutation(s): 0  Gene Names: SAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6SPF0 (Homo sapiens) Explore Q6SPF0  Go to UniProtKB:  Q6SPF0
PHAROS:  Q6SPF0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal(3)malignant brain tumor-like protein 3	B	73	Homo sapiens	Mutation(s): 0  Gene Names: L3MBTL3, KIAA1798, MBT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JM7 (Homo sapiens) Explore Q96JM7  Go to UniProtKB:  Q96JM7
PHAROS:  Q96JM7 GTEx:  ENSG00000198945

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.981	α = 90
b = 95.515	β = 90
c = 65.926	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Cao, Y., Wang, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071204
National Natural Science Foundation of China (NSFC)	China	32125008

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release