2VN8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN RETICULON 4 INTERACTING PROTEIN 1 IN COMPLEX WITH NADPH

Authors :   A. C. W. Pike, K. Guo, J. Elkins, E. Ugochukwu, A. K. Roos, P. Filippakopo F. Von Delft, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, U. Oppermann

Date :   31 Jan 08 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Mitochondrion, Transit Peptide, Receptor Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. W. Pike, K. Guo, J. Elkins, E. Ugochukwu, A. K. Roos, P. Filippakopoulos, F. Von Delft, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, U. Oppermann
Crystal Structure Of Human Reticulon 4 Interacting Protein 1 In Complex With Nadph
To Be Published
PubMed: search

Molecule 1 - RETICULON-4-INTERACTING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Fragment	:	RESIDUES 45-396
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NOGO-INTERACTING MITOCHONDRIAL PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	NA	1	Ligand/Ion	SODIUM ION
4	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CIT	-1	Ligand/Ion	CITRIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:85 , TYR A:183 , THR A:187 , GLY A:212 , SER A:214 , GLY A:215 , GLY A:216 , VAL A:217 , VAL A:235 , SER A:237 , TYR A:255 , ASN A:276 , VAL A:277 , LEU A:300 , VAL A:301 , ALA A:341 , PHE A:342 , PHE A:343 , HIS A:386 , ALA A:387 , ARG A:388 , HOH A:2078 , HOH A:2086 , HOH A:2087 , HOH A:2103 , HOH A:2118 , HOH A:2168 , HOH A:2169 , HOH A:2170 , HOH A:2171 , HOH A:2172 , HOH A:2173 , HOH A:2174	BINDING SITE FOR RESIDUE NDP A 600
2	AC2	SOFTWARE	PRO B:85 , TYR B:183 , THR B:187 , GLY B:212 , SER B:214 , GLY B:215 , GLY B:216 , VAL B:217 , SER B:237 , TYR B:255 , ASN B:276 , VAL B:277 , LEU B:300 , VAL B:301 , ALA B:341 , PHE B:342 , PHE B:343 , HIS B:386 , ALA B:387 , ARG B:388 , HOH B:2042 , HOH B:2064 , HOH B:2096 , HOH B:2097 , HOH B:2099 , HOH B:2100 , HOH B:2101 , HOH B:2102 , HOH B:2103 , HOH B:2104	BINDING SITE FOR RESIDUE NDP B 600
3	AC3	SOFTWARE	THR A:176 , ASN A:394 , CIT A:1398 , HOH A:2167 , HOH A:2177	BINDING SITE FOR RESIDUE NA A1397
4	AC4	SOFTWARE	MET A:128 , TRP B:292 , PHE B:332 , GLY B:335 , VAL B:336 , HIS B:337 , HOH B:2078 , HOH B:2105 , HOH B:2106	BINDING SITE FOR RESIDUE GOL B1397
5	AC5	SOFTWARE	HIS A:79 , THR A:174 , HIS A:175 , THR A:176 , NA A:1397 , HOH A:2167 , HOH A:2175 , HOH A:2176 , HOH A:2177 , HOH A:2178	BINDING SITE FOR RESIDUE CIT A1398

(no "SS Bond" information available for 2VN8)

Asymmetric Unit

No.	Residues
1	Phe A:115	-	Pro A:116
2	Phe B:115	-	Pro B:116

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_076369	R	103	H	RT4I1_HUMAN	Disease (OPA10)	372054380	A/B	R	103	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_076369	R	103	H	RT4I1_HUMAN	Disease (OPA10)	372054380	A	R	103	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_076369	R	103	H	RT4I1_HUMAN	Disease (OPA10)	372054380	B	R	103	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	QOR_ZETA_CRYSTAL	PS01162	Quinone oxidoreductase / zeta-crystallin signature.	RT4I1_HUMAN	205-226	2	A:205-226 B:205-226

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	QOR_ZETA_CRYSTAL	PS01162	Quinone oxidoreductase / zeta-crystallin signature.	RT4I1_HUMAN	205-226	1	A:205-226 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	QOR_ZETA_CRYSTAL	PS01162	Quinone oxidoreductase / zeta-crystallin signature.	RT4I1_HUMAN	205-226	1	- B:205-226

(no "Exon" information available for 2VN8)

Asymmetric 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:358
 aligned with RT4I1_HUMAN | Q8WWV3 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:379
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         
          RT4I1_HUMAN    18 CFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGLNDKNCTGKRVLILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVGGSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV 396
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....e---------------------eeee.....hhhhheeeeee.........eeeeeeeeeeehhhhhhhhh..hhhhhhhhhh.................eeeeeeeee...........eeeee...........eeeee...eee.....hhhhhh.hhhhhhhhhhhhh.............eeeee...hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee....hhhhhhhh.....eeee....hhhhhhhhh.......eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------QOR_ZETA_CRYSTAL      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vn8 A  -5 LYFQS---------------------MAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGLNDKNCTGKRVLILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVGGSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV 396
                                |    -         -      ||47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         
                               -1                     0|                                                                                                                                                                                                                                                                                                                                                               
                                                      45

Chain B from PDB  Type:PROTEIN  Length:355
 aligned with RT4I1_HUMAN | Q8WWV3 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:358
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        
          RT4I1_HUMAN    39 RSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGLNDKNCTGKRVLILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVGGSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV 396
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------ADH_N-2vn8B01 B:71-168                                                                            ------------------------------------------------------------------------------ADH_zinc_N_2-2vn8B03 B:247-393                                                                                                                     --- Pfam domains (1)
           Pfam domains (2) --------------------------------ADH_N-2vn8B02 B:71-168                                                                            ------------------------------------------------------------------------------ADH_zinc_N_2-2vn8B04 B:247-393                                                                                                                     --- Pfam domains (2)
         Sec.struct. author .e---eeee.....hhhhheeeeee.........eeeeeeeeeeehhhhhhhhh..hhhhhhhhhh.................eeeeeeeee...........eeeee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhhh.............eeeee...hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee....hhhhhhhh.....eeee..hhhhhhhhhhh.......eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------QOR_ZETA_CRYSTAL      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vn8 B  -2 QS---MAWVIDKYGKNEVLRFTQNMMMPIIHYPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPGDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHTQAASLPYVALTAWSAINKVGGLNDKNCTGKRVLILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVGGSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMASGPCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV 396
                             |   || 48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        
                            -1   0|                                                                                                                                                                                                                                                                                                                                                               
                                 45

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 '\|'

(no "SCOP Domain" information available for 2VN8)

(no "CATH Domain" information available for 2VN8)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GroES (70)

Family: ADH_N (62)

Homo sapiens (Human) (18)

1a	ADH_N-2vn8B01	B:71-168
1b	ADH_N-2vn8B02	B:71-168

Clan: NADP_Rossmann (1239)

Family: ADH_zinc_N_2 (1)

Homo sapiens (Human) (1)

2a	ADH_zinc_N_2-2vn8B03	B:247-393
2b	ADH_zinc_N_2-2vn8B04	B:247-393

Asymmetric Unit(hide GO term definitions)

Chain A,B (RT4I1_HUMAN | Q8WWV3)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:115 - Pro A:116	[ RasMol ]
		Phe B:115 - Pro B:116	[ RasMol ]

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	2vn8
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Ligands, Modified Residues, Ions (4, 5)

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SS Bonds (0, 0)

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