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7vf2

Human m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI)

Method: ELECTRON MICROSCOPY Dmax: 141.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein virilizer homolog

Homo sapiens

UniProt Q69YN4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–1812 Not recorded Zinc finger CCCH domain-containing protein 13 × 1 （Q5T200） Pre-mRNA-splicing regulator WTAP × 2 （Q15007） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7VF2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7VF5 Human m6A-METTL associated complex (WTAP, VIRMA, and HAKAI) Deposited 2021-09-10 Different oligomeric state Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1812（1812 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7YG4 Structure of WTAP-VIRMA in the m6A writer complex Deposited 2022-07-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 381–1486（1106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VIR_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1812； UniProt 1–1812

Zinc finger CCCH domain-containing protein 13

Homo sapiens

UniProt Q5T200

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1106–1668 Not recorded Protein virilizer homolog × 1 （Q69YN4） Pre-mRNA-splicing regulator WTAP × 2 （Q15007） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name ZC3HD_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–563； UniProt 1106–1668

Pre-mRNA-splicing regulator WTAP

Homo sapiens

UniProt Q15007

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–396 Chain D； UniProt 1–396 Not recorded Protein virilizer homolog × 1 （Q69YN4） Zinc finger CCCH domain-containing protein 13 × 1 （Q5T200） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7VF2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7VF5 Human m6A-METTL associated complex (WTAP, VIRMA, and HAKAI) Deposited 2021-09-10 Different oligomeric state Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–396（396 aa）
Chain D 1–396（396 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7YFJ Crystal structure of human WTAP Deposited 2022-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 130–241（112 aa）
Chain B 130–241（112 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, magnesium nitrate, sodium bromide, PEG6000, glycerol
Resolution 2.40 Å R-free 0.240
7YG4 Structure of WTAP-VIRMA in the m6A writer complex Deposited 2022-07-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–273（273 aa）
Chain E 1–273（273 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9XOE Crystal structure of WTAP 1-50 Deposited 2025-11-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–50（50 aa）
Chain C 1–50（50 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1M HEPES pH7.5, 40% v/v Polyethylene glycol 400
Resolution 1.65 Å R-free 0.256
9XOE Crystal structure of WTAP 1-50 Deposited 2025-11-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–50（50 aa）
Chain D 1–50（50 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1M HEPES pH7.5, 40% v/v Polyethylene glycol 400
Resolution 1.65 Å R-free 0.256
9XOF Crystal structure of WTAP 150-245 Deposited 2025-11-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 150–245（96 aa）
Chain D 150–245（96 aa）
Chain H 150–245（96 aa）
Chain I 150–245（96 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；45% W/V Pentaerythritol Propoxylate (17/8 PO/OH), 100mM Tris pH 8.5.
Resolution 2.79 Å R-free 0.270
9XOF Crystal structure of WTAP 150-245 Deposited 2025-11-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 150–245（96 aa）
Chain C 150–245（96 aa）
Chain G 150–245（96 aa）
Chain J 150–245（96 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；45% W/V Pentaerythritol Propoxylate (17/8 PO/OH), 100mM Tris pH 8.5.
Resolution 2.79 Å R-free 0.270

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FL2D_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–396； UniProt 1–396 Author chain D； PDBConstruct 1–396； UniProt 1–396

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7vf2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7vf2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7vf2
Deposition date deposition_date2021-09-10
Structure title titleHuman m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI)
Keywords keywordsm6A-METTL associated complex, cryo-EM, WTAP, Virma., RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.51 Å
Radius of gyration Rg (electron density) rg_electron40.77 Å
Forward intensity I(0) i0553264000.00
Molecular weight molecular_weight193610.0 kDa
Excluded volume excluded_volume243290 ų
Envelope volume envelope_volume326650 ų
Hydration-shell volume shell_volume67323 ų
Envelope diameter envelope_diameter150.2 Å
Shell Rg shell_rg45.80 Å
Envelope Rg envelope_rg40.72 Å
Shape Rg shape_rg40.78 Å
Total Rg total_rg41.01 Å
Total atoms total_atoms13565
Residues n_residues1716
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax141.1 Å
Rg (real space) rg_real41.51 Å
Rg uncertainty (real space) rg_real_error1.26 Å
I(0) (real space) i0_real5.5330e+08
I(0) uncertainty (real space) i0_real_error9.6910e+06
Rg (reciprocal space) rg_reciprocal41.51 Å
I(0) (reciprocal space) i0_reciprocal553300000.0000
Solution quality estimate total_estimate0.8712
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.3 Å
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.176
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha54210000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.870
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)