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Title :   STRUCTURE OF AN EXTRACELLULAR GIANT HEMOGLOBIN OF THE GUTLESS BEARD WORM OLIGOBRACHIA MASHIKOI

Authors :   N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, K. Miki

Date :   12 Sep 05 (Deposition) - 25 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (6x)

Keywords :   Giant Hemoglobin, Sulfide Binding, Invertebrate, Pogonophora, Oligobrachia Mashikoi, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, K. Miki
Structure Of An Extracellular Giant Hemoglobin Of The Gutless Beard Worm Oligobrachia Mashikoi.
Proc. Natl. Acad. Sci. Usa V. 102 14521 2005
PubMed-ID: 16204001 | Reference-DOI: 10.1073/PNAS.0501541102
(for further references see the PDB file header)

Molecule 1 - GIANT HEMOGLOBIN, A1(B) GLOBIN CHAIN
	Chains	:	A
	Organism Scientific	:	OLIGOBRACHIA MASHIKOI
	Organism Taxid	:	55676
	Synonym	:	HEMOGLOBIN CHAIN A1

Molecule 2 - GIANT HEMOGLOBIN, A2(A5) GLOBIN CHAIN
	Chains	:	B
	Organism Scientific	:	OLIGOBRACHIA MASHIKOI
	Organism Taxid	:	55676
	Synonym	:	HEMOGLOBIN CHAIN A2

Molecule 3 - GIANT HEMOGLOBIN, B2(C) GLOBIN CHAIN
	Chains	:	C
	Organism Scientific	:	OLIGOBRACHIA MASHIKOI
	Organism Taxid	:	55676
	Synonym	:	HEMOGLOBIN CHAIN B2

Molecule 4 - GIANT HEMOGLOBIN, B1(D) GLOBIN CHAIN
	Chains	:	D
	Organism Scientific	:	OLIGOBRACHIA MASHIKOI
	Organism Taxid	:	55676
	Synonym	:	HEMOGLOBIN CHAIN B1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (6x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	OXY	4	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 1 (2, 48)

No.	Name	Count	Type	Full Name
1	HEM	24	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	OXY	24	Ligand/Ion	OXYGEN MOLECULE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:45 , PHE A:46 , VAL A:49 , HIS A:62 , ARG A:65 , VAL A:66 , ALA A:69 , HIS A:94 , ARG A:97 , LEU A:99 , ASN A:103 , PHE A:104 , MET A:107 , TYR A:131 , ILE A:138 , OXY A:201 , HIS D:91 , GLN D:95	BINDING SITE FOR RESIDUE HEM A 200
2	AC2	SOFTWARE	PHE A:32 , PHE A:46 , HIS A:62 , VAL A:66 , MET A:107 , HEM A:200	BINDING SITE FOR RESIDUE OXY A 201
3	AC3	SOFTWARE	LEU B:45 , PHE B:46 , ARG B:48 , VAL B:49 , HIS B:62 , ARG B:65 , LEU B:70 , GLN B:93 , HIS B:94 , ARG B:97 , ILE B:99 , GLY B:103 , TYR B:104 , PHE B:107 , OXY B:1201 , HIS C:93 , GLN C:97	BINDING SITE FOR RESIDUE HEM B 200
4	AC4	SOFTWARE	TRP B:32 , VAL B:66 , HEM B:200	BINDING SITE FOR RESIDUE OXY B 1201
5	AC5	SOFTWARE	ARG B:89 , GLN B:93 , LEU C:49 , PHE C:50 , VAL C:53 , HIS C:66 , ARG C:69 , GLN C:97 , HIS C:98 , ARG C:101 , VAL C:104 , HIS C:108 , PHE C:109 , MET C:112 , ILE C:143 , HOH C:1001 , OXY C:2201	BINDING SITE FOR RESIDUE HEM C 200
6	AC6	SOFTWARE	PHE C:36 , PHE C:50 , HIS C:66 , VAL C:70 , HEM C:200	BINDING SITE FOR RESIDUE OXY C 2201
7	AC7	SOFTWARE	HIS A:89 , GLN A:93 , VAL D:45 , MET D:49 , PHE D:50 , GLN D:64 , ARG D:67 , GLN D:95 , HIS D:96 , ILE D:99 , VAL D:102 , VAL D:107 , LEU D:110 , SER D:111 , ILE D:141 , OXY D:3201	BINDING SITE FOR RESIDUE HEM D 200
8	AC8	SOFTWARE	GLN D:64 , VAL D:68 , HEM D:200	BINDING SITE FOR RESIDUE OXY D 3201

Asymmetric Unit

No.	Residues
1	A:2	-	A:130
2	A:121	-	C:126
3	B:2	-	B:132
4	C:4	-	C:135
5	D:3	-	D:133

(no "Cis Peptide Bond" information available for 2D2M)

(no "SAP(SNP)/Variant" information available for 2D2M)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	GLBA1_OLIMA	22-151	1	A:6-135
				GLBB1_OLIMA	27-154	1	D:11-138
				GLBB2_OLIMA	34-157	1	C:18-141

Biological Unit 1 (1, 18)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	GLBA1_OLIMA	22-151	6	A:6-135
				GLBB1_OLIMA	27-154	6	D:11-138
				GLBB2_OLIMA	34-157	6	C:18-141

(no "Exon" information available for 2D2M)

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:140
 aligned with GLBA1_OLIMA | Q7M419 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:140
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156
          GLBA1_OLIMA    17 VCNRLEQILVKTQWAQSYGEAENRAAFSRDLFSELFNIQGSSRALFSGVGVDDMNSAAFTAHCLRVTGALNRLISQLDQQATINADLAHLAGQHASRNLDASNFAAMGQAVMSVVPTHLDCFNQHAWGECYERIASGISG 156
               SCOP domains d2d2ma_ A: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----GLOBIN  PDB: A:6-135 UniProt: 22-151                                                                                              ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d2m A   1 VCNRLEQILVKTQWAQSYGEAENRAAFSRDLFSELFNIQGSSRALFSGVGVDDMNSAAFTAHCLRVTGALNRLISQLDQQATINADLAHLAGQHASRNLDASNFAAMGQAVMSVVPTHLDCFNQHAWGECYERIASGISG 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with GLBA2_OLIMA | Q7M413 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:142
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156  
          GLBA2_OLIMA    17 DCTSLNRLLVKRQWAEAYGEGTNRELLGNRIWEDLFANMPDARGLFSRVNGNDIDSSEFQAHSLRVLGGLDMCVASLDDVPVLNALLARLNSQHDSRGIPAAGYPAFVASAISAVRATVGARSFDNDAWNSCMNQIVSGISG 158
               SCOP domains d2d2mb_ B: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d2m B   1 DCTSLNRLLVKRQWAEAYGEGTNRELLGNRIWEDLFANMPDARGLFSRVNGNDIDSSEFQAHSLRVLGGLDMCVASLDDVPVLNALLARLNSQHDSRGIPAAGYPAFVASAISAVRATVGARSFDNDAWNSCMNQIVSGISG 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:146
 aligned with GLBB2_OLIMA | Q7M418 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:146
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157      
          GLBB2_OLIMA    18 SCCSSEDRANVMHNWDAAWSAAYSDRRVALAQAVFASLFSRDAAAQGLFSGVSADNPDSADFRAHCVRVVNGLDVAINMLNDPAVLNEQLAHLSAQHQARAGVAAAHFDVMAEAFAEVMPQVSSCFSSDSWNRCFARIANGISAGL 163
               SCOP domains d2d2mc_ C: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------GLOBIN  PDB: C:18-141 UniProt: 34-157                                                                                       ------ PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d2m C   2 SCCSSEDRANVMHNWDAAWSAAYSDRRVALAQAVFASLFSRDAAAQGLFSGVSADNPDSADFRAHCVRVVNGLDVAINMLNDPAVLNEQLAHLSAQHQARAGVAAAHFDVMAEAFAEVMPQVSSCFSSDSWNRCFARIANGISAGL 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with GLBB1_OLIMA | Q5KSB7 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:145
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156     
          GLBB1_OLIMA    17 ECCSRGDAEVVISEWDQVFNAAMAGSSESAVGVAIFDAFFASSGVSPSMFPGGGDSNNPEFLAQVSRVVSGADIAINSLTNRATCDSLLSHLNAQHRAISGVTGAAVTHLSQAISSVVAQVLPSAHIDAWEYCMAYIAAGIGAGL 161
               SCOP domains d2d2md_ D: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------GLOBIN  PDB: D:11-138 UniProt: 27-154                                                                                           ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d2m D   1 ECCSRGDAEVVISEWDQVFNAAMAGSSESAVGVAIFDAFFASSGVSPSMFPGGGDSNNPEFLAQVSRVVSGADIAINSLTNRATCDSLLSHLNAQHRAISGVTGAAVTHLSQAISSVVAQVLPSAHIDAWEYCMAYIAAGIGAGL 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: automated matches (42)

Protein domain: automated matches (42)

Oligobrachia mashikoi [TaxId: 55676] (4)

1a	d2d2ma_	A:
1b	d2d2mb_	B:
1c	d2d2mc_	C:
1d	d2d2md_	D:

(no "CATH Domain" information available for 2D2M)

(no "Pfam Domain" information available for 2D2M)

Asymmetric Unit(hide GO term definitions)

Chain A (GLBA1_OLIMA | Q7M419)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B (GLBA2_OLIMA | Q7M413)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain C (GLBB2_OLIMA | Q7M418)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain D (GLBB1_OLIMA | Q5KSB7)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2d2m)

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	2d2m
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UniProtKB/Swiss-Prot
	GLBA1_OLIMA \| Q7M419	:	2d2n 2zfo 2zs0 2zs1
	GLBA2_OLIMA \| Q7M413	:	2d2n 2zfo 2zs0 2zs1
	GLBB1_OLIMA \| Q5KSB7	:	2d2n 2zfo 2zs0 2zs1
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2d2n	THE SAME PROTEIN, HG DERIVATIVE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (5, 5)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 36)

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Related Entries Specified in the PDB File