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- PDB-2gtl: Lumbricus Erythrocruorin at 3.5A resolution -

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Basic information

Entry
Database: PDB / ID: 2gtl
TitleLumbricus Erythrocruorin at 3.5A resolution
Components
  • (Extracellular globin ...) x 2
  • (Extracellular hemoglobin linker ...) x 2
  • Extracellular globin-3
  • Hemoglobin chain d1
  • Hemoglobin linker chain L1
KeywordsOXYGEN STORAGE/TRANSPORT / Annelid erythrocruorins / respiratory protein / hexagonal bilayer / dihedral D6 symmetry / triple stranded helical coils / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding
Similarity search - Function
Lipocalin - #620 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1520 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1530 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1540 / Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin ...Lipocalin - #620 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1520 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1530 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1540 / Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin / Low-density lipoprotein receptor domain class A / Myoglobin-like, M family globin domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Lipocalin / Helix non-globular / Globin-like superfamily / Special / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Extracellular globin / Extracellular globin-2 / Extracellular globin-3 / Extracellular globin-4 / Extracellular hemoglobin linker L3 subunit / Extracellular hemoglobin linker L2 subunit / Hemoglobin linker chain L1
Similarity search - Component
Biological speciesLumbricus terrestris (common earthworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRoyer Jr., W.E. / Sharma, H. / Strand, K. / Knapp, J.E. / Bhyravbhatla, B.
CitationJournal: Structure / Year: 2006
Title: Lumbricus erythrocruorin at 3.5 a resolution: architecture of a megadalton respiratory complex.
Authors: Royer Jr., W.E. / Sharma, H. / Strand, K. / Knapp, J.E. / Bhyravbhatla, B.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE Authors state that the conflicts at residue 78 for chains A,E,I and residue 66 for chains ...SEQUENCE Authors state that the conflicts at residue 78 for chains A,E,I and residue 66 for chains B,F,J are possibly due to an error with the sequencing, however they can not distinguish it at the current resolution.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular globin 4
B: Extracellular globin 2
C: Extracellular globin-3
D: Hemoglobin chain d1
E: Extracellular globin 4
F: Extracellular globin 2
G: Extracellular globin-3
H: Hemoglobin chain d1
I: Extracellular globin 4
J: Extracellular globin 2
K: Extracellular globin-3
L: Hemoglobin chain d1
M: Hemoglobin linker chain L1
N: Extracellular hemoglobin linker L2 subunit
O: Extracellular hemoglobin linker L3 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,90544
Polymers275,94615
Non-polymers7,96029
Water00
1
A: Extracellular globin 4
B: Extracellular globin 2
C: Extracellular globin-3
D: Hemoglobin chain d1
E: Extracellular globin 4
F: Extracellular globin 2
G: Extracellular globin-3
H: Hemoglobin chain d1
I: Extracellular globin 4
J: Extracellular globin 2
K: Extracellular globin-3
L: Hemoglobin chain d1
M: Hemoglobin linker chain L1
N: Extracellular hemoglobin linker L2 subunit
O: Extracellular hemoglobin linker L3 subunit
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)3,406,864528
Polymers3,311,347180
Non-polymers95,516348
Water0
TypeNameSymmetry operationNumber
point symmetry operation12
2


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: Extracellular globin 4
B: Extracellular globin 2
C: Extracellular globin-3
D: Hemoglobin chain d1
E: Extracellular globin 4
F: Extracellular globin 2
G: Extracellular globin-3
H: Hemoglobin chain d1
I: Extracellular globin 4
J: Extracellular globin 2
K: Extracellular globin-3
L: Hemoglobin chain d1
M: Hemoglobin linker chain L1
N: Extracellular hemoglobin linker L2 subunit
O: Extracellular hemoglobin linker L3 subunit
hetero molecules
x 24


  • crystal asymmetric unit
  • 6.81 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)6,813,7271056
Polymers6,622,695360
Non-polymers191,032696
Water0
TypeNameSymmetry operationNumber
transform to crystal frame2
point symmetry operation12
Unit cell
Length a, b, c (Å)176.080, 257.960, 436.530
Angle α, β, γ (deg.)89.69, 97.15, 90.98
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 622 / Schoenflies symbol: D6 (2x6 fold dihedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.99023, -0.05197, -0.12941), (0.13788, 0.50422, 0.85249), (0.02095, -0.86201, 0.50646)-1.65217, -0.21834, -1.62163
3generate(0.96326, 0.03047, -0.26682), (0.24739, -0.48728, 0.83747), (-0.1045, -0.87271, -0.47692)-0.97235, -2.11336, -1.50619
4generate(0.94509, 0.21433, -0.24673), (0.21122, -0.97665, -0.03931), (-0.24939, -0.01496, -0.96829)-2.21643, -2.89465, -0.66088
5generate(0.96357, 0.24689, -0.10282), (0.03602, -0.50074, -0.86485), (-0.26501, 0.82964, -0.49139)0.75781, -0.56749, 2.44098
6generate(0.99015, 0.13997, 0.00339), (-0.06781, 0.5006, -0.86302), (-0.1225, 0.85429, 0.50516)1.48809, -0.05652, 0.63077
7generate(-0.94957, -0.10498, 0.29545), (-0.11909, -0.75091, -0.64958), (0.29005, -0.652, 0.70054)-1.00599, -2.30478, -0.37744
8generate(-0.95529, -0.23565, 0.17856), (-0.22231, 0.17434, -0.95926), (0.19492, -0.95607, -0.21893)-0.78939, 0.48797, -1.11833
9generate(-0.97696, -0.20833, 0.04643), (-0.21239, 0.92733, -0.30815), (0.02114, -0.31092, -0.9502)-2.34257, 1.94545, 0.94172
10generate(-0.99714, -0.072, -0.02307), (-0.06884, 0.73831, 0.67094), (-0.03127, 0.6706, -0.74116)-1.67681, -0.16198, 2.09542
11generate(-0.9977, 0.04861, 0.04718), (0.03646, -0.20168, 0.97877), (0.0571, 0.97824, 0.19945)0.0939, -1.78915, 2.07663
12generate(-0.97557, 0.04895, 0.21419), (0.02321, -0.94645, 0.322), (0.21848, 0.31911, 0.92219)-0.87521, -3.00517, 0.40173
13generate(0.98952, 0.14395, 0.01155), (-0.14429, 0.98878, 0.03853), (-0.00587, -0.03979, 0.99919)63.79785, 132.8392, 216.14185
14generate(0.99992, -0.00666, 0.01072), (-0.00612, 0.48763, 0.87303), (-0.01104, -0.87302, 0.48755)61.71643, 131.91033, 214.2694
15generate(0.98349, -0.08354, -0.16051), (0.09716, -0.50451, 0.85792), (-0.15265, -0.85935, -0.48807)61.33404, 130.41609, 214.5674
16generate(0.95755, 0.05902, -0.28216), (0.05721, -0.99825, -0.01466), (-0.28253, -0.0021, -0.95926)57.77668, 130.23473, 216.2495
17generate(0.94342, 0.22925, -0.23959), (-0.09733, -0.49924, -0.86098), (-0.31699, 0.83558, -0.44868)58.87162, 131.28099, 218.29621
18generate(0.96321, 0.25183, -0.09383), (-0.21213, 0.4981, -0.84077), (-0.16499, 0.82975, 0.5332)63.17867, 132.7596, 216.58716
19generate(-0.94724, -0.23945, 0.21306), (0.03929, -0.74647, -0.66426), (0.3181, -0.62084, 0.7165)59.0542, 130.5702, 215.35065
20generate(-0.97741, -0.2065, 0.04495), (-0.08279, 0.17843, -0.98046), (0.19445, -0.96204, -0.1915)57.47877, 133.24688, 215.8687
21generate(-0.9975, -0.06491, -0.02786), (-0.05212, 0.94257, -0.32991), (0.04768, -0.32763, -0.9436)59.69155, 133.26482, 216.46762
22generate(-0.99803, 0.04768, 0.04079), (0.06275, 0.76382, 0.64238), (-0.00053, 0.64367, -0.7653)62.93848, 132.24233, 217.8886
23generate(-0.97661, 0.05894, 0.20678), (0.19408, -0.17233, 0.96573), (0.09256, 0.98327, 0.15686)62.01574, 129.82776, 218.08703
24generate(-0.94671, -0.09532, 0.30767), (0.19344, -0.93202, 0.30647), (0.25754, 0.34965, 0.90079)60.90111, 128.8195, 216.69973

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Components

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Extracellular globin ... , 2 types, 6 molecules AEIBFJ

#1: Protein Extracellular globin 4 / Globin IV / Erythrocruorin / Globin A


Mass: 17566.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / References: UniProt: P13579
#2: Protein Extracellular globin 2 / Globin II / Erythrocruorin / Globin AIII / Globin B


Mass: 16268.229 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / References: UniProt: P02218

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Protein , 3 types, 7 molecules CGKDHLM

#3: Protein Extracellular globin-3 / Extracellular globin III / Erythrocruorin / Globin C


Mass: 17331.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / References: UniProt: P11069
#4: Protein Hemoglobin chain d1


Mass: 15988.263 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / References: UniProt: O61233
#5: Protein Hemoglobin linker chain L1


Mass: 24936.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / References: UniProt: Q9GV76

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Extracellular hemoglobin linker ... , 2 types, 2 molecules NO

#6: Protein Extracellular hemoglobin linker L2 subunit


Mass: 25057.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / References: UniProt: Q2I743
#7: Protein Extracellular hemoglobin linker L3 subunit


Mass: 24486.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / References: UniProt: Q2I742

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Non-polymers , 4 types, 29 molecules

#8: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO
#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 6% (w/w) PEG 8000, 10mM CaCl2, 3% isopropanol, 60mM Hepes, pH 7.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. all: 1718296 / Num. obs: 890862 / % possible obs: 89.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.078
Reflection shellResolution: 3.5→3.63 Å / % possible all: 74.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→100 Å / FOM work R set: 0.786 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.297 38554 RANDOM in resolution shells
Rwork0.288 --
obs0.288 775689 -
all-960925 -
Displacement parametersBiso mean: 68.78 Å2
Refinement stepCycle: LAST / Resolution: 3.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19103 0 545 0 19648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.5-3.520.4175600.4281078511345
3.52-3.550.4166160.4071115211768
3.55-3.570.3965890.4071117911768
3.57-3.60.4246130.3951152112134
3.6-3.630.3936090.3791179312402
3.63-3.650.3916470.381181712464
3.65-3.680.3656480.3771202812676
3.68-3.710.3686250.3681185712482
3.71-3.740.366760.3591230412980
3.74-3.770.3796710.3591210812779
3.77-3.80.3626550.3561227612931
3.8-3.840.366380.3471267113309
3.84-3.870.3336350.3491252213157
3.87-3.910.3636710.3391296013631
3.91-3.940.3416210.3411292513546
3.94-3.980.3497300.341320213932
3.98-4.020.3317340.3281355514289
4.02-4.060.3347600.321374314503
4.06-4.10.347220.3141415814880
4.1-4.150.317170.3121424714964
4.15-4.20.3127820.3091454615328
4.2-4.250.3237330.3081475515488
4.25-4.30.2938200.2941501515835
4.3-4.350.2957490.2851515615905
4.35-4.410.2837850.2791559316378
4.41-4.470.288250.2751558516410
4.47-4.530.2938460.2821583116677
4.53-4.60.2758330.2681613216965
4.6-4.670.2968340.2721610116935
4.67-4.750.2928880.271640017288
4.75-4.830.2818810.2621638717268
4.83-4.920.2758490.2681662917478
4.92-5.010.2879420.2691658917531
5.01-5.120.2828200.2651676817588
5.12-5.230.2818530.2661688017733
5.23-5.350.298880.2651710617994
5.35-5.480.2788800.2571691617796
5.48-5.630.2678830.2561706317946
5.63-5.80.2768580.2571711017968
5.8-5.980.2739100.2561722518135
5.98-6.20.2629060.2481726218168
6.2-6.450.2419230.231742318346
6.45-6.740.2518940.2291749118385
6.74-7.10.2239090.2161748318392
7.1-7.540.2269100.2151767618586
7.54-8.120.2369070.2281759418501
8.12-8.940.2368520.2381628617138
8.94-10.230.2657650.2621471515480
10.23-12.890.3017230.2911415514878
12.89-1000.3937690.4141446015229

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