Structure of PDB 7xss Chain B

Receptor sequence

>7xssB (length=1282) Species: 237368 (Candidatus Scalindua brodae)

DMNITVELTFFEPYRLVEWFDWDARKKSHSAMRGQAFAQWTWKGKGRTAG
KSFITGTLVRSAVIKAVEELLSLNNGKWEGVPCCNGSFQTDESKGKKPSF
LRKRHTLQWQANNKNICDKEEACPFCILLGRFDNAGKVHERNKDYDIHFS
NFDLDHKQEKNDLRLVDIASGRILNRVDFDTGKAKDYFRTWEADYETYGT
YTGRITLRNEHAKKLLLASLGFVDKLCGALCRIEVIKSEDHNDELRKQAE
VIVEAFKQNDKLEKIRILADAIRTLRLHGEGVIEKDELPDGKEERDKGHH
LWDIKVQGTALRTKLKELWQSNKDIGWRKFTEMLGSNLYLIYKKETGGVS
TRFRILGDTEYYSKDSEGSDLFIPVTPPEGIETKEWIIVGRLKAATPFYF
GVQQPSDSIPGKEKKSEDSLVINEHTSFNILLDKENRYRIPRSALRGALR
RDLRTAFGSGCNVSLGGQILCNCKVCIEMRRITLKDSVSDFSEPPEIRYR
IAKNPGTATVEDGSLFDIEVGPEGLTFPFVLRYRGHKFPEQLSSVIRYWE
ENDGKNGMAWLGGLDSTGKGRFALKDIKIFEWDLNQKINEYIKERGMRGK
EKELLEMGESSLPDGLIPYKFFEERECLFPYKENLKPQWSEVQYTIEVGS
PLLTADTISALTEPGNRDAIAYKKRVYNDGNNAIEPEPRFAVKSETHRGI
FRTAVGRRTGDLGKEDHEDCTCDMCIIFGNEHESSKIRFEDLELINGNEF
EKLEKHIDHVAIDRFTGGALDKAKFDTYPLAGSPKKPLKLKGRFWIKKGF
SGDHKLLITTALSDIRDGLYPLGSKGGVGYGWVAGISIDDNVPDDFKEMI
NGPINNDYVHPGHQSPKQDHKNKNIYYPHYFLDSGSKVYREKDIITHEEF
TEELLSGKINCKLETLTPLIIPDTSDENGLKLQGNKPGHKNYKFFNINGE
LMIPGSELRGMLRTHFEALTKSCFAIFGEDSTKTLGGKLDKALHPCTGLS
DGLCPGCHLFGTTDYKGRVKFGFAKYENGPEWLITRGNNPERSLTLGVLE
SPRPAFSIPDDESEIPGRKFYLHHNGWRIIRQKQLEIRETVQPERNVTTE
VMDKGNVFSFDVRFENLREWELGLLLQSLDPGKNIAHKLGKGKPYGFGSV
KIKIDSLHTFKINSNNDKIKRVPQSDIREYINKGYQKLIEWSGNNSIQKG
NVLPQWHVIPHIDKLYKLLWVPFLNDSKLEPDVRYPVLNEESKGYIEGSD
YTYKKLGDKDNLPYKTRVKGLTTPWSPWNPFQ

3D structure

• PDB: 7xss Target RNA activates the protease activity of Craspase to confer antiviral defense.
• Chain: B
• Resolution: 3.2 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	B	K187 K292 R294 K320 R323 Y367 K371 R382 D542 G543 S544 L545 F546 D749 E761 H762 D801 K802 K804 F805 T1423 L1459 E1460 S1461 R1505 L1648	K183 K264 R266 K292 R295 Y339 K343 R354 D512 G513 S514 L515 F516 D719 E731 H732 D771 K772 K774 F775 T1013 L1049 E1050 S1051 R1095 L1238
BS02	rna	B	E16 W23 R37 Q39 F41 T45 F57 T59 L62 R64 S91 Q93 T94 K101 P102 S103 F104 L105 R106 R108 L133 G134 K141 H143 Y149 H152 F153 N155 D157 I177 L178 N179 G186 K187 A188 F192 K229 Y389 S391 G431 Q433 R472 S473 R476 R481 S494 L495 L500 T513 L514 Y529 R530 I531 K533 F546 G592 L594 S596 A685 R728 I730 R732 N760 S765 D788 H789 V790 I792 R794 K804 F805 S854 Y922 P967 S1001 E1002 R1004 R1008 G1421 T1422 T1423 L1459 E1460 P1462 R1463 F1466 Y1481 K1551 K1553 P1554 Y1645 V1647 Y1663	E12 W19 R33 Q35 F37 T41 F53 T55 L58 R60 S87 Q89 T90 K97 P98 S99 F100 L101 R102 R104 L129 G130 K137 H139 Y145 H148 F149 N151 D153 I173 L174 N175 G182 K183 A184 F188 K225 Y361 S363 G401 Q403 R442 S443 R446 R451 S464 L465 L470 T483 L484 Y499 R500 I501 K503 F516 G562 L564 S566 A655 R698 I700 R702 N730 S735 D758 H759 V760 I762 R764 K774 F775 S824 Y877 P922 S956 E957 R959 R963 G1011 T1012 T1013 L1049 E1050 P1052 R1053 F1056 Y1071 K1141 K1143 P1144 Y1235 V1237 Y1253
BS03	ZN	B	C501 C503 C506	C471 C473 C476
BS04	ZN	B	H747 C750 C752 C755	H717 C720 C722 C725
BS05	ZN	B	C1406 C1414 C1417	C996 C1004 C1007
BS06	ZN	B	C88 C121 C130	C84 C117 C126

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0051607 defense response to virus

External links

• PDB: RCSB:7xss, PDBe:7xss, PDBj:7xss
• PDBsum: 7xss
• PubMed: 36306795
• UniProt: A0A0B0EGF3