MAPK variant effect atlas
Proteins / ARAF

ARAF

Serine/threonine-protein kinase A-Raf

RAF kinase UniProt P10398 HSP90 client (literature): strong 3D structure ↓ 24 interaction partners · volcano ↗
Mutagenized 2–296Mutagenized 298–604RBD 19–91RBDCRD 98–144CRDKinase 310–570Kinase1604 aagrey box: mutagenized region

Abundance under HSP90 inhibition (pimitespib). The HSP90 calls compare each variant's inhibited and untreated abundance. Scores are WT-relative: 1 = wild type.

12,674 variantsmissense decreased 37% · increased 2%HSP90-dependent 99% of missense & deletionsbuffered 21% · poorly buffered 18% · WT-like or increased 61%
Other cells fade; highlighted cells are outlined.
Annotation tracks
Structure
Function
Chaperone
Variant effect
Track legend & definitions
Secondary structure
alpha helix3-10 helixpi helixbeta strandbeta bridgeturnbendno_ss
DSSP assignment on the reference structure.
Relative SASA
0.000.250.500.751.00
Side-chain solvent accessibility (0 = buried, 1 = fully exposed). The pipeline calls a residue surface-exposed above 0.25.
pLDDT
50.062.575.087.5100.0
AlphaFold per-residue confidence. The analysis drops residues below 60.
Curated feature
Protein-protein interfaceCatalytic / active siteLigand / substrate pocketRegulatory elementOther annotation
UniProt / literature annotation, coloured by class. Red marks a curated protein-protein interface — the independent comparison for our predicted interfaces.
Annotated interface
yesno
Curated protein-interface residue, independent of any structure prediction in this study.
Active site
yesno
Curated catalytic / active-site residue.
Inter-domain contact
yesno
Residue contacting another domain of the same protein (all-atom), so a variant effect there may be intramolecular rather than at a PPI.
HSP90 contact
TrueFalseUnknown
Contacts HSP90 in the chaperone-client cryo-EM structures ('Unknown' where the protein was not mapped).
CDC37 contact
TrueFalseUnknown
Contacts CDC37. These positions report kinase foldability rather than a canonical binding surface.
Fraction buffered
0%25%50%75%100%
Fraction of variants at this position that are buffered: wild-type-like untreated but decreased under HSP90 inhibition (HSP90i condition only).
Fraction HSP90-dependent
0%25%50%75%100%
Fraction of variants at this position whose abundance falls under HSP90 inhibition by at least the wild-type-to-synonymous gap (the paper's dependence call; HSP90i condition only).
Fraction decreased
0%25%50%75%100%
Fraction of variants at this position classified decreased in this assay (2.5th-percentile rule).
Fraction increased
0%25%50%75%100%
Fraction of variants at this position classified increased in this assay.
Domain Secondary structure Relative SASA pLDDT Curated feature Annotated interface Active site Inter-domain contact HSP90 contact CDC37 contact Fraction buffered Fraction HSP90-dependent Fraction decreased Fraction increased Interface A V I L G F Y W C M P S T N Q D E H K R * -
RBD CRD Kinase 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 0.46 1.00 2.00
Click a position for its interactions and annotations — ■ the Interface strip marks positions in ≥1 supported interface (darker = more partners)

Structure · ARAF alone

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Interfaces of ARAF

One row per interface: complexes of the same pair and source whose interfaces overlap (IoU ≥ 0.3) are merged, as in the Fig. 6c,d volcano plots (median Cohen's d; q from the geometric-mean p). Supported: at least one complex with q < 0.05 and |d| ≥ 0.2 in either basal assay.

PartnerSourceActivity dq Abundance dqInterface positionsSupported
CRAFAF-M-0.751.6e-54-0.090.26614supportedStructure ↗
BRAFAF-M-0.779.6e-50-0.250.00511supportedStructure ↗
KSR1AF-M-0.835.8e-49+0.020.44413supportedStructure ↗
KSR2AF-M-0.701.6e-47+0.050.10314supportedStructure ↗
EGFRRF2-PPI-0.883.6e-40-0.090.1829supportedStructure ↗
SFNAF-M+2.218.1e-24+0.340.1108supportedStructure ↗
RABGGTBRF2-PPI+2.606.0e-23+0.405.1e-108supportedStructure ↗
RRASAF-M+0.020.477+0.621.0e-218supportedStructure ↗
RRAS2AF-M+0.348.1e-11+0.327.0e-2114supportedStructure ↗
NRASAF-M+0.341.6e-09+0.339.9e-2014supportedStructure ↗
KRASAF-M+0.342.0e-09+0.311.8e-1914supportedStructure ↗
MEK2RF2-PPI-0.191.0e-10-0.343.3e-1717supportedStructure ↗
HRASAF-M+0.343.7e-09+0.283.8e-1713supportedStructure ↗
YWHAGAF-M+1.971.1e-16+0.350.1878supportedStructure ↗
YWHAZRF2-PPI+2.962.3e-15+0.270.0025supportedStructure ↗
MAP2K3AF-M-0.534.3e-14-0.306.6e-068supportedStructure ↗
MAP2K5AF-M-0.461.2e-13-0.329.4e-0811supportedStructure ↗
A0A1B0GUL7RF2-PPI-0.301.5e-08-0.294.7e-1217supportedStructure ↗
YWHAHRF2-PPI+2.602.8e-10+0.120.4444supportedStructure ↗
STK11AF-M-0.381.4e-08-0.238.4e-0412supportedStructure ↗
YWHAZAF-M+1.361.9e-08+0.150.64413supportedStructure ↗
YWHABAF-M+1.235.4e-08+0.180.36014supportedStructure ↗
YWHAHAF-M+1.352.9e-07+0.120.78012supportedStructure ↗
YWHAEAF-M+1.312.9e-07+0.170.62512supportedStructure ↗
MEK1RF2-PPI-0.384.2e-07-0.160.0098supportedStructure ↗
YWHAQAF-M+1.255.0e-06+0.140.73912supportedStructure ↗
MEK2AF-M-0.230.003-0.235.0e-0514supportedStructure ↗
MEK1AF-M-0.230.007-0.237.5e-0514supportedStructure ↗