2LGF - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF CA2+/CALMODULIN COMPLEXED WITH A PEPTIDE REPRESENTING THE CALMODULIN-BINDING DOMAIN OF L-SELECTIN

Authors :   J. L. Gifford, H. Ishida, H. J. Vogel

Date :   25 Jul 11 (Deposition) - 13 Jun 12 (Release) - 27 Apr 16 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B
NMR Structure *: A,B  (1x)

Keywords :   Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Gifford, H. Ishida, H. J. Vogel
Structural Insights Into Calmodulin-Regulated L-Selectin Ectodomain Shedding.
J. Biol. Chem. V. 287 26513 2012
PubMed-ID: 22711531 | Reference-DOI: 10.1074/JBC.M112.373373

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET30B(+)
	Fragment	:	SEQUENCE DATABASE RESIDUES 4-149
	Gene	:	CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CAM

Molecule 2 - L-SELECTIN
	Chains	:	B
	Engineered	:	YES
	Fragment	:	SEQUENCE DATABASE RESIDUES 349-363
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CD62 ANTIGEN-LIKE FAMILY MEMBER L, LEUKOCYTE ADHESION MOLECULE 1, LAM-1, LEUKOCYTE SURFACE ANTIGEN LEU-8, LEUKOCYTE- ENDOTHELIAL CELL ADHESION MOLECULE 1, LECAM1, LYMPH NODE HOMING RECEPTOR, TQ1, GP90-MEL
	Synthetic	:	YES

		1	2
NMR Structure	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

NMR Structure * (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

NMR Structure (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31	BINDING SITE FOR RESIDUE CA A 401
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67	BINDING SITE FOR RESIDUE CA A 402
3	AC3	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104	BINDING SITE FOR RESIDUE CA A 403
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140	BINDING SITE FOR RESIDUE CA A 404

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

(no "Cis Peptide Bond" information available for 2LGF)

NMR Structure (15, 15)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_069222	N	54	I	CALM1_HUMAN	Disease (CPVT4)	267607276	A	N	53	I
02	UniProt	VAR_073275	F	90	L	CALM1_HUMAN	Disease (LQT14)	730882253	A	F	89	L
03	UniProt	VAR_073276	D	96	V	CALM2_HUMAN	Disease (LQT15)	730882254	A	D	95	V
04	UniProt	VAR_073277	N	98	I	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	I
05	UniProt	VAR_078541	N	98	S	CALM1_HUMAN	Disease (CPVT4)	398124647	A	N	97	S
06	UniProt	VAR_078543	N	98	S	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	S
07	UniProt	VAR_078261	A	103	V	CALM3_HUMAN	Disease	---	A	A	102	V
08	UniProt	VAR_078542	D	130	G	CALM1_HUMAN	Disease (LQT14)	730882252	A	D	129	G
09	UniProt	VAR_078544	D	130	G	CALM2_HUMAN	Disease (LQT15)	730882252	A	D	129	G
10	UniProt	VAR_078262	D	130	V	CALM2_HUMAN	Disease (LQT15)	---	A	D	129	V
11	UniProt	VAR_073279	D	132	E	CALM2_HUMAN	Disease (LQT15)	398124648	A	D	131	E
12	UniProt	VAR_073280	D	134	H	CALM2_HUMAN	Disease (LQT15)	398124650	A	D	133	H
13	UniProt	VAR_073281	Q	136	P	CALM2_HUMAN	Disease (LQT15)	398124649	A	Q	135	P
14	UniProt	VAR_078263	E	141	G	CALM1_HUMAN	Disease (LQT14)	---	A	E	140	G
15	UniProt	VAR_073282	F	142	L	CALM1_HUMAN	Disease (LQT14)	11551462	A	F	141	L

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

NMR Structure * (15, 15)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_069222	N	54	I	CALM1_HUMAN	Disease (CPVT4)	267607276	A	N	53	I
02	UniProt	VAR_073275	F	90	L	CALM1_HUMAN	Disease (LQT14)	730882253	A	F	89	L
03	UniProt	VAR_073276	D	96	V	CALM2_HUMAN	Disease (LQT15)	730882254	A	D	95	V
04	UniProt	VAR_073277	N	98	I	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	I
05	UniProt	VAR_078541	N	98	S	CALM1_HUMAN	Disease (CPVT4)	398124647	A	N	97	S
06	UniProt	VAR_078543	N	98	S	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	S
07	UniProt	VAR_078261	A	103	V	CALM3_HUMAN	Disease	---	A	A	102	V
08	UniProt	VAR_078542	D	130	G	CALM1_HUMAN	Disease (LQT14)	730882252	A	D	129	G
09	UniProt	VAR_078544	D	130	G	CALM2_HUMAN	Disease (LQT15)	730882252	A	D	129	G
10	UniProt	VAR_078262	D	130	V	CALM2_HUMAN	Disease (LQT15)	---	A	D	129	V
11	UniProt	VAR_073279	D	132	E	CALM2_HUMAN	Disease (LQT15)	398124648	A	D	131	E
12	UniProt	VAR_073280	D	134	H	CALM2_HUMAN	Disease (LQT15)	398124650	A	D	133	H
13	UniProt	VAR_073281	Q	136	P	CALM2_HUMAN	Disease (LQT15)	398124649	A	Q	135	P
14	UniProt	VAR_078263	E	141	G	CALM1_HUMAN	Disease (LQT14)	---	A	E	140	G
15	UniProt	VAR_073282	F	142	L	CALM1_HUMAN	Disease (LQT14)	11551462	A	F	141	L

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

NMR Structure (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM1_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CALM2_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CALM3_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM1_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM2_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM3_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

NMR Structure * (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM1_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CALM2_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
				CALM3_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM1_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM2_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM3_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

(no "Exon" information available for 2LGF)

NMR Structure

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:146
 aligned with CALM1_HUMAN | P0DP23 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
          CALM1_HUMAN     4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------S-------------------------------G------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------S-------------------------------V------------------- SAPs(SNPs) (3)
                PROSITE (2) ----EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lgf A   3 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain A from PDB  Type:PROTEIN  Length:146
 aligned with CALM2_HUMAN | P0DP24 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
          CALM2_HUMAN     4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------S-------------------------------G------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------S-------------------------------V------------------- SAPs(SNPs) (3)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (3)
                PROSITE (4) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (5)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lgf A   3 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain A from PDB  Type:PROTEIN  Length:146
 aligned with CALM3_HUMAN | P0DP25 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
          CALM3_HUMAN     4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------S-------------------------------G------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------S-------------------------------V------------------- SAPs(SNPs) (3)
                PROSITE (1) ----EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (6)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lgf A   3 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with LYAM1_HUMAN | P14151 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:15
                                   358     
          LYAM1_HUMAN   349 AFIIWLARRLKKGKK 363
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 2lgf B 349 AFIIWLARRLKKGKK 363
                                   358

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 2LGF)

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

(no "Pfam Domain" information available for 2LGF)

NMR Structure(hide GO term definitions)

Chain A (CALM3_HUMAN | P0DP25)

Chain A (CALM1_HUMAN | P0DP23)

Chain A (CALM2_HUMAN | P0DP24)

Chain B (LYAM1_HUMAN | P14151)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0050839	cell adhesion molecule binding	Interacting selectively and non-covalently with a cell adhesion molecule.
	GO:0043208	glycosphingolipid binding	Interacting selectively and non-covalently with glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0033198	response to ATP	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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	Cis Peptide Bonds
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	2lgf
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	614916
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	616247
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	616249
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(no "Related Entries Specified in the PDB File" available for 2LGF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (15, 15)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (95, 97)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File