Experimental structure
9E3R
Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome
Original coordinates
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Coordinate coverage
Mapped chains
Label and author chain identifiers are kept separately. Observed Cα counts refer to each mapped annotation core.
| Protein | Label chain | Author chain | Domain | Observed Cα / core | Observed substitutions |
|---|---|---|---|---|---|
| DNMT3A | U | ["U"] | UP:Q9Y6K1:PWWP1 | 0 / 59 | 0 |
| DNMT3A | V | ["Y"] | UP:Q9Y6K1:PWWP1 | 0 / 59 | 0 |
| DNMT3A | Y | ["W"] | UP:Q9Y6K1:PWWP1 | 0 / 59 | 0 |
| DNMT3A | Z | ["K"] | UP:Q9Y6K1:PWWP1 | 0 / 59 | 0 |
| DNMT3B | S | ["V"] | UP:Q9UBC3:PWWP1 | 0 / 59 | 0 |
| DNMT3B | T | ["Z"] | UP:Q9UBC3:PWWP1 | 0 / 59 | 0 |
| DNMT3B | W | ["L"] | UP:Q9UBC3:PWWP1 | 0 / 59 | 0 |
| DNMT3B | X | ["X"] | UP:Q9UBC3:PWWP1 | 0 / 59 | 0 |
Chemical identity
Chemical components and interpretation
Geometry, with defined scope
Independent contact evidence
Inspect 22 retained contact records
| CCD / instance | Protein chain | Contact class | Minimum core / broader domain distance Å |
|---|---|---|---|
| SAH · GA | DNMT3A · U | noncore contact in multidomain chain | — / — |
| SAH · HA | DNMT3A · V | noncore contact in multidomain chain | — / — |
| SAH · RA | DNMT3A · Y | noncore contact in multidomain chain | — / — |
| SAH · VA | DNMT3A · Z | noncore contact in multidomain chain | — / — |
| ZN · AA | DNMT3B · S | noncore contact in multidomain chain | — / — |
| ZN · BA | DNMT3B · S | noncore contact in multidomain chain | — / — |
| ZN · CA | DNMT3B · S | noncore contact in multidomain chain | — / — |
| ZN · DA | DNMT3A · U | noncore contact in multidomain chain | — / — |
| ZN · EA | DNMT3A · U | noncore contact in multidomain chain | — / — |
| ZN · FA | DNMT3A · U | noncore contact in multidomain chain | — / — |
| ZN · IA | DNMT3A · V | noncore contact in multidomain chain | — / — |
| ZN · JA | DNMT3A · V | noncore contact in multidomain chain | — / — |
| ZN · KA | DNMT3A · V | noncore contact in multidomain chain | — / — |
| ZN · LA | DNMT3B · W | noncore contact in multidomain chain | — / — |
| ZN · MA | DNMT3B · W | noncore contact in multidomain chain | — / — |
| ZN · NA | DNMT3B · W | noncore contact in multidomain chain | — / — |
| ZN · OA | DNMT3A · Y | noncore contact in multidomain chain | — / — |
| ZN · PA | DNMT3A · Y | noncore contact in multidomain chain | — / — |
| ZN · QA | DNMT3A · Y | noncore contact in multidomain chain | — / — |
| ZN · SA | DNMT3A · Z | noncore contact in multidomain chain | — / — |
| ZN · TA | DNMT3A · Z | noncore contact in multidomain chain | — / — |
| ZN · UA | DNMT3A · Z | noncore contact in multidomain chain | — / — |
Biological partners
Histone H3.2 · histone or histone peptide · label chains ["A","E","I","M"]
Histone H4 · histone or histone peptide · label chains ["B","F","J","N"]
Histone H2A · histone or histone peptide · label chains ["C","G","K","O"]
Histone H2B · histone or histone peptide · label chains ["D","H","L","P"]
DNA (320-MER) · nucleic acid · label chains ["Q"]
DNA (319-MER) · nucleic acid · label chains ["R"]
Isoform 3 of DNA (cytosine-5)-methyltransferase 3B · protein/peptide · label chains ["S","T","W","X"]
DNA (cytosine-5)-methyltransferase 3A · protein/peptide · label chains ["U","V","Y","Z"]
Source interpretation
Focused scientific audit
retain with stated interpretation/caveats. Associated deposition only: no mapped PWWP atoms; source title explicitly describes PWWP-deleted DNMT3A2/3B3. Exclusion from observed-PWWP denominator is correct.