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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA HFQ IN COMPLEX WITH ADPNP

Authors :   A. D. Nikulin, V. N. Murina, A. G. Gabdulkhakov

Date :   24 Feb 11 (Deposition) - 08 Feb 12 (Release) - 28 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Lsm, Rna-Binding Protein, Srna, Mrna, Rna Chaperone, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Murina, N. Lekontseva, A. Nikulin
Hfq Binds Ribonucleotides In Three Different Rna-Binding Sites.
Acta Crystallogr. , Sect. D V. 69 1504 2013
PubMed-ID: 23897473 | Reference-DOI: 10.1107/S090744491301010X

Molecule 1 - PROTEIN HFQ
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HFQ, PA4944
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ADE	1	Ligand/Ion	ADENINE
2	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	ANP	3	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:25 , THR A:61 , VAL A:63 , HOH A:90 , HOH A:125 , HOH A:137 , HOH A:180 , ILE F:30 , GLN F:52	BINDING SITE FOR RESIDUE ADP A 101
2	AC2	SOFTWARE	LEU A:26 , ILE A:30 , GLN A:52 , HOH A:92 , TYR B:25 , GLY B:29 , SER B:60 , THR B:61 , VAL B:63 , HOH B:142	BINDING SITE FOR RESIDUE ADP B 101
3	AC3	SOFTWARE	ILE B:30 , GLN B:52 , ARG B:69 , TYR C:25 , GLY C:29 , THR C:61	BINDING SITE FOR RESIDUE ADP C 101
4	AC4	SOFTWARE	ARG A:19 , LYS A:47 , GLN C:52 , TYR D:25 , GLY D:29 , LYS D:31 , THR D:61 , VAL D:63 , HOH D:99 , HOH D:128 , HOH D:206	BINDING SITE FOR RESIDUE ANP D 101
5	AC5	SOFTWARE	HIS C:57 , GLN D:8 , GLN D:41 , PHE D:42 , HIS D:57 , HOH D:85 , HOH D:92 , HOH D:95 , HOH D:184 , HOH D:185 , HOH D:190 , HIS E:57	BINDING SITE FOR RESIDUE ANP D 102
6	AC6	SOFTWARE	GLU D:18 , PRO D:21 , SER D:65 , ARG D:66 , HOH D:208 , GLU E:18 , ARG E:66	BINDING SITE FOR RESIDUE PEG D 103
7	AC7	SOFTWARE	THR A:49 , VAL A:50 , TYR B:25 , SER B:65 , HOH B:88 , LEU D:32 , GLN D:52 , TYR E:25 , LYS E:31 , THR E:61 , HOH E:87 , HOH E:94 , HOH E:98 , HOH E:108 , HOH E:121	BINDING SITE FOR RESIDUE ANP E 101
8	AC8	SOFTWARE	ASN B:48 , LEU E:32 , GLN E:52 , TYR F:25 , THR F:61 , VAL F:63	BINDING SITE FOR RESIDUE ADE F 101

(no "SS Bond" information available for 3QUI)

(no "Cis Peptide Bond" information available for 3QUI)

(no "SAP(SNP)/Variant" information available for 3QUI)

(no "PROSITE Motif" information available for 3QUI)

(no "Exon" information available for 3QUI)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:71
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:71
                                    11        21        31        41        51        61        71 
             HFQ_PSEAE    2 SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPS 72
               SCOP domains d3quia_ A: Pleiotropic translational regulator Hfq                      SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3qui A  2 SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPS 72
                                    11        21        31        41        51        61        71

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:67
                                    13        23        33        43        53        63       
             HFQ_PSEAE    4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
               SCOP domains d3quib_ B: Pleiotropic translational regulator Hfq                  SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..eeeeee....eeeeeeeee...eeeee....eeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3qui B  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    13        23        33        43        53        63

Chain C from PDB  Type:PROTEIN  Length:69
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:69
                                    11        21        31        41        51        61         
             HFQ_PSEAE    2 SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
               SCOP domains d3quic_ C: Pleiotropic translational regulator Hfq                    SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.eeeeee....eeeeeeeee...eeeee....eeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  3qui C  2 SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    11        21        31        41        51        61

Chain D from PDB  Type:PROTEIN  Length:67
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:67
                                    15        25        35        45        55        65       
             HFQ_PSEAE    6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPS 72
               SCOP domains d3quid_ D: Pleiotropic translational regulator Hfq                  SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3qui D  6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPS 72
                                    15        25        35        45        55        65

Chain E from PDB  Type:PROTEIN  Length:67
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:67
                                    13        23        33        43        53        63       
             HFQ_PSEAE    4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
               SCOP domains d3quie_ E: Pleiotropic translational regulator Hfq                  SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3qui E  4 GHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    13        23        33        43        53        63

Chain F from PDB  Type:PROTEIN  Length:65
 aligned with HFQ_PSEAE | Q9HUM0 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:65
                                    15        25        35        45        55        65     
             HFQ_PSEAE    6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
               SCOP domains d3quif_ F: Pleiotropic translational regulator Hfq                SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeee....eeeeeeeee...eeeee...eeeee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3qui F  6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRL 70
                                    15        25        35        45        55        65

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Sm-like fold (103)

Superfamily: Sm-like ribonucleoproteins (95)

Family: Pleiotropic translational regulator Hfq (28)

Protein domain: Pleiotropic translational regulator Hfq (13)

Pseudomonas aeruginosa [TaxId: 287] (9)

1a	d3quia_	A:
1b	d3quib_	B:
1c	d3quic_	C:
1d	d3quid_	D:
1e	d3quie_	E:
1f	d3quif_	F:

(no "CATH Domain" information available for 3QUI)

(no "Pfam Domain" information available for 3QUI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (HFQ_PSEAE | Q9HUM0)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qui)

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	3qui
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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	HFQ_PSEAE \| Q9HUM0
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		Domain Information	:	XDom
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UniProtKB/Swiss-Prot
	HFQ_PSEAE \| Q9HUM0	:	1u1s 1u1t 3inz 3m4g 4j5y 4j6w 4j6x 4j6y 4mmk 4mml

1hk9	E. COLI HFQ
1u1s	WILD-TYPE P.AERUGINOSA HFQ AT ANOTHER CRYSTALLISATION CONDITION
1u1t	WILD-TYPE P.AERUGINOSA HFQ
3gib	E. COLI HFQ IN COMPLEX WITH POLY(A)
3inz	P. AERUGINOSA HFQ, H57T MUTANT
3m4g	P. AERUGINOSA HFQ, H57A MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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