4V93 | pdb_00004v93

Fitted coordinates for Lumbricus terrestris hemoglobin cryo-EM complex (EMD-2627)

PDB DOI: https://doi.org/10.2210/pdb4V93/pdb
Entry: 4V93 supersedes: 4CYX, 4D0H, 4D0I
EM Map EMD-2627: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Lumbricus terrestris
Mutation(s): No

Deposited: 2014-04-16 Released: 2014-07-09
Deposition Author(s): Chen, W.T., Chen, Y.C., Liou, H.H., Chao, C.Y.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis for Cooperative Oxygen Binding and Bracelet-Assisted Assembly of Lumbricus Terrestris Hemoglobin

Chen, W.T., Chen, Y.C., Liou, H.H., Chao, C.Y.

To be published.

Macromolecule Content

Total Structure Weight: 3,529.19 kDa
Atom Count: 231,000
Modeled Residue Count: 28,740
Deposited Residue Count: 31,116
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR GLOBIN-3	A [auth A0] DB [auth Av] EA [auth AW] F [auth A5] JA [auth Ab] A [auth A0], DB [auth Av], EA [auth AW], F [auth A5], JA [auth Ab], K [auth AC], OA [auth Ag], P [auth AH], TA [auth Al], U [auth AM], YA [auth Aq], Z [auth AR]	149	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for P11069 (Lumbricus terrestris) Explore P11069 Go to UniProtKB: P11069
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11069
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN CHAIN D1	AA [auth AS] B [auth A1] EB [auth Aw] FA [auth AX] G [auth A6] AA [auth AS], B [auth A1], EB [auth Aw], FA [auth AX], G [auth A6], KA [auth Ac], L [auth AD], PA [auth Ah], Q [auth AI], UA [auth Am], V [auth AN], ZA [auth Ar]	140	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for O61233 (Lumbricus terrestris) Explore O61233 Go to UniProtKB: O61233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O61233
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR GLOBIN-4	AB [auth As] BA [auth AT] BB [auth At] C [auth A2] CA [auth AU] AB [auth As], BA [auth AT], BB [auth At], C [auth A2], CA [auth AU], D [auth A3], FB [auth Ax], GA [auth AY], GB [auth Ay], H [auth A7], HA [auth AZ], I [auth AA], LA [auth Ad], M [auth AE], MA [auth Ae], N [auth AF], QA [auth Ai], R [auth AJ], RA [auth Aj], S [auth AK], VA [auth An], W [auth AO], WA [auth Ao], X [auth AP]	147	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for P13579 (Lumbricus terrestris) Explore P13579 Go to UniProtKB: P13579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13579
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR GLOBIN-2	AC [auth BK] CB [auth Au] DA [auth AV] DD [auth Bn] E [auth A4] AC [auth BK], CB [auth Au], DA [auth AV], DD [auth Bn], E [auth A4], EC [auth BO], ED [auth Bo], FC [auth BP], HB [auth Az], IA [auth Aa], ID [auth Bs], J [auth AB], JC [auth BT], JD [auth Bt], KB [auth B2], KC [auth BU], LB [auth B3], NA [auth Af], ND [auth Bx], O [auth AG], OC [auth BY], OD [auth By], PB [auth B7], PC [auth BZ], QB [auth BA], SA [auth Ak], T [auth AL], TC [auth Bd], UB [auth BE], UC [auth Be], VB [auth BF], XA [auth Ap], Y [auth AQ], YC [auth Bi], ZB [auth BJ], ZC [auth Bj]	145	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for P02218 (Lumbricus terrestris) Explore P02218 Go to UniProtKB: P02218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02218
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN CHAIN D1	BD [auth Bl] CC [auth BM] DF [auth Cf] EE [auth CG] GD [auth Bq] BD [auth Bl], CC [auth BM], DF [auth Cf], EE [auth CG], GD [auth Bq], HC [auth BR], IB [auth B0], IF [auth Ck], JE [auth CL], LD [auth Bv], MC [auth BW], NB [auth B5], NF [auth Cp], OE [auth CQ], RC [auth Bb], SB [auth BC], SF [auth Cu], TE [auth CV], UD [auth C4], WC [auth Bg], XB [auth BH], XF [auth Cz], YE [auth Ca], ZD [auth CB]	158	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for O61233 (Lumbricus terrestris) Explore O61233 Go to UniProtKB: O61233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O61233
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR GLOBIN-4	CD [auth Bm] DC [auth BN] HD [auth Br] IC [auth BS] JB [auth B1] CD [auth Bm], DC [auth BN], HD [auth Br], IC [auth BS], JB [auth B1], MD [auth Bw], NC [auth BX], OB [auth B6], SC [auth Bc], TB [auth BD], XC [auth Bh], YB [auth BI]	151	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for P13579 (Lumbricus terrestris) Explore P13579 Go to UniProtKB: P13579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13579
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR GLOBIN-3	AD [auth Bk] BC [auth BL] CF [auth Ce] DE [auth CF] FD [auth Bp] AD [auth Bk], BC [auth BL], CF [auth Ce], DE [auth CF], FD [auth Bp], GC [auth BQ], HF [auth Cj], IE [auth CK], KD [auth Bu], LC [auth BV], MB [auth B4], MF [auth Co], NE [auth CP], PD [auth Bz], QC [auth Ba], RB [auth BB], RF [auth Ct], SE [auth CU], TD [auth C3], VC [auth Bf], WB [auth BG], WF [auth Cy], XE [auth CZ], YD [auth CA]	170	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for P11069 (Lumbricus terrestris) Explore P11069 Go to UniProtKB: P11069
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11069
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN LINKER CHAIN L1	AE [auth CC] EF [auth Cg] FE [auth CH] JF [auth Cl] KE [auth CM] AE [auth CC], EF [auth Cg], FE [auth CH], JF [auth Cl], KE [auth CM], OF [auth Cq], PE [auth CR], QD [auth C0], TF [auth Cv], UE [auth CW], VD [auth C5], ZE [auth Cb]	240	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for Q9GV76 (Lumbricus terrestris) Explore Q9GV76 Go to UniProtKB: Q9GV76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GV76
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT	AF [auth Cc] BE [auth CD] FF [auth Ch] GE [auth CI] KF [auth Cm] AF [auth Cc], BE [auth CD], FF [auth Ch], GE [auth CI], KF [auth Cm], LE [auth CN], PF [auth Cr], QE [auth CS], RD [auth C1], UF [auth Cw], VE [auth CX], WD [auth C6]	288	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for Q2I743 (Lumbricus terrestris) Explore Q2I743 Go to UniProtKB: Q2I743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2I743
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT	BF [auth Cd] CE GF [auth Ci] HE [auth CJ] LF [auth Cn] BF [auth Cd], CE, GF [auth Ci], HE [auth CJ], LF [auth Cn], ME [auth CO], QF [auth Cs], RE [auth CT], SD [auth C2], VF [auth Cx], WE [auth CY], XD [auth C7]	240	Lumbricus terrestris	Mutation(s): 0
UniProt
Find proteins for Q2I742 (Lumbricus terrestris) Explore Q2I742 Go to UniProtKB: Q2I742
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2I742
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

This entry supersedes: 4CYX, 4D0H, 4D0I

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2014-12-10
Changes: Other
Version 1.2: 2019-08-21
Changes: Data collection, Database references, Other
Version 1.3: 2019-12-11
Changes: Other
Version 1.4: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

4V93 | pdb_00004v93

Fitted coordinates for Lumbricus terrestris hemoglobin cryo-EM complex (EMD-2627)

Literature

Structural Basis for Cooperative Oxygen Binding and Bracelet-Assisted Assembly of Lumbricus Terrestris Hemoglobin

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)