HEADER RNA 12-JAN-25 9LHK TITLE FOCUSED ASYMMETRIC UNIT OF ENV38-GOLLD RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENV38-GOLLD RNA; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED CAUDOVIRALES PHAGE; SOURCE 3 ORGANISM_TAXID: 2100421; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS NATURAL RNA NANOCAGES; LARGE RNA; CRYO-EM; GOLLD RNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR K.ZHANG,S.LI REVDAT 2 29-OCT-25 9LHK 1 JRNL REVDAT 1 10-SEP-25 9LHK 0 JRNL AUTH S.ZHANG,R.YI,L.AN,J.LIU,X.YAO,S.LI,K.ZHANG JRNL TITL STRUCTURAL INSIGHTS INTO HIGHER-ORDER NATURAL RNA-ONLY JRNL TITL 2 MULTIMERS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 32 2012 2025 JRNL REFN ESSN 1545-9985 JRNL PMID 40770114 JRNL DOI 10.1038/S41594-025-01650-1 REMARK 2 REMARK 2 RESOLUTION. 2.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.930 REMARK 3 NUMBER OF PARTICLES : 589456 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9LHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055665. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : FOCUSED ASYMMETRIC UNIT OF REMARK 245 ENV38-GOLLD RNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4600.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G G 1 REMARK 465 G G 2 REMARK 465 A G 495 REMARK 465 C G 496 REMARK 465 C G 497 REMARK 465 A G 498 REMARK 465 A G 499 REMARK 465 A G 500 REMARK 465 C G 501 REMARK 465 U G 502 REMARK 465 U G 503 REMARK 465 A G 504 REMARK 465 U G 505 REMARK 465 A G 506 REMARK 465 U G 507 REMARK 465 U G 508 REMARK 465 U G 509 REMARK 465 G G 510 REMARK 465 C G 511 REMARK 465 A G 512 REMARK 465 U G 513 REMARK 465 U G 514 REMARK 465 U G 515 REMARK 465 A G 516 REMARK 465 G G 517 REMARK 465 G G 518 REMARK 465 A G 519 REMARK 465 U G 520 REMARK 465 U G 521 REMARK 465 G G 522 REMARK 465 C G 523 REMARK 465 A G 524 REMARK 465 A G 525 REMARK 465 A G 526 REMARK 465 A G 527 REMARK 465 U G 528 REMARK 465 C G 529 REMARK 465 A G 530 REMARK 465 U G 531 REMARK 465 A G 532 REMARK 465 A G 533 REMARK 465 A G 534 REMARK 465 A G 535 REMARK 465 A G 536 REMARK 465 U G 537 REMARK 465 C G 538 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O6 G G 330 N3 U G 350 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 C G 11 N1 C G 11 C6 -0.038 REMARK 500 A G 204 C5 A G 204 N7 -0.041 REMARK 500 A G 219 N9 A G 219 C4 -0.036 REMARK 500 A G 572 N9 A G 572 C4 -0.039 REMARK 500 A G 582 N9 A G 582 C4 0.037 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C G 8 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 C G 8 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 C G 8 C6 - N1 - C1' ANGL. DEV. = -7.7 DEGREES REMARK 500 C G 8 C2 - N1 - C1' ANGL. DEV. = 9.5 DEGREES REMARK 500 C G 18 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C G 18 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 C G 18 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 C G 18 C2 - N1 - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 U G 30 C2 - N1 - C1' ANGL. DEV. = 7.9 DEGREES REMARK 500 C G 32 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 C G 32 C2 - N1 - C1' ANGL. DEV. = 6.8 DEGREES REMARK 500 U G 53 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 U G 53 C2 - N1 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 U G 69 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 U G 69 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 U G 69 C2 - N1 - C1' ANGL. DEV. = 9.1 DEGREES REMARK 500 C G 74 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 U G 79 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 G G 86 C4 - N9 - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 C G 98 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 C G 98 C2 - N1 - C1' ANGL. DEV. = 7.8 DEGREES REMARK 500 U G 100 C6 - N1 - C1' ANGL. DEV. = -9.8 DEGREES REMARK 500 U G 100 C2 - N1 - C1' ANGL. DEV. = 9.8 DEGREES REMARK 500 G G 103 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 U G 117 C2 - N1 - C1' ANGL. DEV. = 8.1 DEGREES REMARK 500 U G 119 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 U G 125 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 U G 125 N3 - C2 - O2 ANGL. DEV. = -7.4 DEGREES REMARK 500 U G 125 C2 - N1 - C1' ANGL. DEV. = 9.2 DEGREES REMARK 500 U G 129 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 U G 129 N3 - C2 - O2 ANGL. DEV. = -6.5 DEGREES REMARK 500 U G 129 C2 - N1 - C1' ANGL. DEV. = 8.8 DEGREES REMARK 500 U G 130 N3 - C2 - O2 ANGL. DEV. = -6.4 DEGREES REMARK 500 U G 133 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 U G 135 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 U G 135 C6 - N1 - C1' ANGL. DEV. = -10.0 DEGREES REMARK 500 U G 135 C2 - N1 - C1' ANGL. DEV. = 10.7 DEGREES REMARK 500 G G 138 C6 - C5 - N7 ANGL. DEV. = -3.9 DEGREES REMARK 500 U G 151 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 U G 176 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 U G 176 C2 - N1 - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 C G 177 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 C G 177 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 C G 177 C2 - N1 - C1' ANGL. DEV. = 7.9 DEGREES REMARK 500 G G 181 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 C G 182 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 A G 183 O3' - P - OP1 ANGL. DEV. = 7.7 DEGREES REMARK 500 G G 197 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES REMARK 500 G G 197 N7 - C8 - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 G G 197 C8 - N9 - C4 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 161 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63100 RELATED DB: EMDB REMARK 900 FOCUSED ASYMMETRIC UNIT OF ENV38-GOLLD RNA DBREF 9LHK G 1 833 PDB 9LHK 9LHK 1 833 SEQRES 1 G 833 G G A U G G C C G C C U A SEQRES 2 G 833 U G G U C G U C A A A U A SEQRES 3 G 833 A A C U A C G A A A G U A SEQRES 4 G 833 G G A U A A A G U G G A A SEQRES 5 G 833 U A G U A A G G U U U A G SEQRES 6 G 833 C U A U U C U G C G G U U SEQRES 7 G 833 U C A U C U U G U A A A G SEQRES 8 G 833 A U G G A G C U U G A G U SEQRES 9 G 833 A G G C A A G U G A G A U SEQRES 10 G 833 A U C A A U U U U U C U U SEQRES 11 G 833 A G U A U G U G A G G G U SEQRES 12 G 833 A A C A C U U U A G C A G SEQRES 13 G 833 A G G A G A A A A G U U G SEQRES 14 G 833 A C U G G G U C U U U G C SEQRES 15 G 833 A G A G A U U C A G U U G SEQRES 16 G 833 A G U U C G G A A G A G C SEQRES 17 G 833 A A U A A G A A U A A C U SEQRES 18 G 833 C A U A G A A U U C A A U SEQRES 19 G 833 G C G A G A G G U A G G G SEQRES 20 G 833 A A C U A A U C C C U C C SEQRES 21 G 833 C U A U A A U C G C G G U SEQRES 22 G 833 A U U C A A U A U G A U A SEQRES 23 G 833 G U U U A C U U A A C A U SEQRES 24 G 833 C A A A U U G G G G A A A SEQRES 25 G 833 C C C U U U A A G A U A A SEQRES 26 G 833 G A U A G U G U A C G G G SEQRES 27 G 833 U G G U G C C G U U A U U SEQRES 28 G 833 A U C C U U U G A U A G A SEQRES 29 G 833 G U G U A C C A G C A C C SEQRES 30 G 833 U A U C G A U G A A G U A SEQRES 31 G 833 A A C U U G G A A U A U G SEQRES 32 G 833 G U G G U A G G G A U A C SEQRES 33 G 833 C A C A U C G G G U A G U SEQRES 34 G 833 U A A G U A U U C U G U C SEQRES 35 G 833 G U U C A A A A G G C G G SEQRES 36 G 833 C G G A G C U U G U G A U SEQRES 37 G 833 A G A C C G C U A C C U G SEQRES 38 G 833 A A A C C A C U G C A A A SEQRES 39 G 833 A C C A A A C U U A U A U SEQRES 40 G 833 U U G C A U U U A G G A U SEQRES 41 G 833 U G C A A A A U C A U A A SEQRES 42 G 833 A A A U C A A A A U A A G SEQRES 43 G 833 A A A A A G U G U C U A U SEQRES 44 G 833 C A G U U U U G A C C G A SEQRES 45 G 833 A A G G U G U C U A C A U SEQRES 46 G 833 A G U A A U G A G U U G U SEQRES 47 G 833 U C A U U G C C A C A A A SEQRES 48 G 833 C A C U C U C A A G G U G SEQRES 49 G 833 A A U G U G A U U C U U U SEQRES 50 G 833 C G A A A G G U U U C U A SEQRES 51 G 833 A C A C C G C A A G U G U SEQRES 52 G 833 G A A U C U G C U C G G C SEQRES 53 G 833 A G G G U A G A A G A A A SEQRES 54 G 833 A U A A G U A A G A A G A SEQRES 55 G 833 G A G U A G G U U A A A A SEQRES 56 G 833 C U C A A A G A G U G G U SEQRES 57 G 833 U C A C U U A A A U A A C SEQRES 58 G 833 C G A C A U U G G U U G U SEQRES 59 G 833 U A C A U C U C A A A A G SEQRES 60 G 833 G A U G U G G A A A C A A SEQRES 61 G 833 A G G G A A U A G A U A A SEQRES 62 G 833 U C C U U U U A A A G A C SEQRES 63 G 833 A A C U A C A A U A U G G SEQRES 64 G 833 U G U A U U C U C A G C C SEQRES 65 G 833 U CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 TER 16827 U G 833 MASTER 253 0 0 0 0 0 0 616826 1 0 65 END