[English] 日本語
Yorodumi
- PDB-6z2m: H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z2m
TitleH11-D4, SARS-CoV-2 RBD, CR3022 ternary complex
Components
  • (CR3022 antibody) x 2
  • Spike glycoprotein
  • nanobody D4
KeywordsVIRAL PROTEIN / Antibody / nanobody complex / rbd
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsNaismith, J.H. / Ren, J. / Zhou, D. / Zhao, Y. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100209/Z/12/Z United Kingdom
Engineering and Physical Sciences Research CouncilEP/S025243/1. United Kingdom
CitationJournal: To Be Published
Title: Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2
Authors: Naismith, J.H.
History
DepositionMay 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike glycoprotein
B: CR3022 antibody
C: CR3022 antibody
E: Spike glycoprotein
H: CR3022 antibody
L: CR3022 antibody
F: nanobody D4
D: nanobody D4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,90210
Polymers166,4608
Non-polymers4422
Water00
1
A: Spike glycoprotein
B: CR3022 antibody
C: CR3022 antibody
D: nanobody D4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4515
Polymers83,2304
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Spike glycoprotein
H: CR3022 antibody
L: CR3022 antibody
F: nanobody D4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4515
Polymers83,2304
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.717, 150.395, 119.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 22115.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Protein CR3022 antibody


Mass: 22874.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody CR3022 antibody


Mass: 24186.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody nanobody D4


Mass: 14052.671 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Purified RBD, Fab CR3022 and nanobody H11-D4 were mixed together at a molar ratio of 1:1:1 to a final concentration of approximately 7 mg/ml and incubated at room temperature for one hour. ...Details: Purified RBD, Fab CR3022 and nanobody H11-D4 were mixed together at a molar ratio of 1:1:1 to a final concentration of approximately 7 mg/ml and incubated at room temperature for one hour. Initial screening was performed in 96-well plates using the nanolitre sitting-drop vapour diffusion method. The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.71→106.1 Å / Num. obs: 73071 / % possible obs: 99 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.065 / Net I/σ(I): 7.4
Reflection shellResolution: 2.71→2.76 Å / Redundancy: 9 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 3426 / CC1/2: 0.087 / Rpim(I) all: 3.953 / % possible all: 94

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YZ7

6yz7


Resolution: 2.71→74.86 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 2365 4.99 %
Rwork0.1983 45047 -
obs0.2004 47412 64.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.92 Å2 / Biso mean: 53.5819 Å2 / Biso min: 11.46 Å2
Refinement stepCycle: final / Resolution: 2.71→74.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11699 0 28 0 11727
Biso mean--70.23 --
Num. residues----1516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.71-2.770.289350.2988951002
2.77-2.830.4119360.379747150712
2.83-2.890.3867410.336276180219
2.89-2.970.3558470.3204997104424
2.97-3.050.3781420.30771264130630
3.05-3.140.3256950.29161544163938
3.14-3.240.29891170.27541985210249
3.24-3.350.29771260.26192480260661
3.35-3.490.32561590.25052953311272
3.49-3.650.26622000.22183376357683
3.65-3.840.29121720.20764015418797
3.84-4.080.25472140.190841194333100
4.08-4.390.22032100.164141104320100
4.39-4.840.16872380.147341354373100
4.84-5.530.19131860.165941984384100
5.54-6.970.23342460.200741854431100
6.97-74.860.22292310.19054359459099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.83970.8253-0.66432.35760.92284.4238-0.09270.38780.7183-0.44720.086-0.6446-0.90610.0734-0.24430.40110.04080.13670.65560.15720.491712.709748.040649.9923
23.14841.0326-2.42826.5753-2.40584.85790.0805-0.17111.206-0.26740.0385-0.14320.0440.1141-0.11640.12460.080.14190.48310.04180.504123.167139.156645.3228
35.8064-1.6961-1.63450.82350.77380.72590.9291.62291.0128-0.7020.03180.8049-0.7377-0.9859-0.15870.57730.32-0.02761.03380.33250.476514.799339.587435.1974
42.76740.5962-1.32442.44590.18923.6668-0.16650.8275-0.4068-0.16290.1942-0.21770.5458-0.1973-0.0560.2561-0.01980.06910.3491-0.05990.340513.186231.841256.6216
53.6950.0429-1.00691.9984-0.28993.9439-0.0308-0.0677-0.15220.08650.1147-0.06620.07160.0703-0.07250.1545-0.02780.03950.2966-0.02150.263910.847134.302864.5598
61.4141-3.26470.51777.6473-0.20968.84110.41471.9086-0.3169-1.3042-0.01370.5983-0.14470.1023-0.01430.6725-0.2246-0.00641.19130.14050.82767.425443.595634.2127
71.4611-0.43850.08061.53710.56791.37130.2186-0.4182-0.2954-0.001-0.0513-0.22570.2996-0.3478-0.09530.2064-0.04930.02070.16780.05820.263436.152724.044737.6237
81.4667-0.14180.22440.6552-1.02411.5752-0.0711-0.1403-0.49250.2633-0.03310.25830.9238-0.5176-0.05940.3846-0.0685-0.00760.23710.030.293827.889817.012433.1507
92.23850.35780.47111.7470.22190.14260.0591-0.4407-0.7970.43580.03140.39940.6234-0.3546-0.04930.3928-0.4510.0770.25490.5830.238727.434317.0244.2507
102.01990.2170.14071.60540.98671.5029-0.0415-0.4701-0.41660.04910.18970.32250.4393-0.21790.00580.4046-0.0152-0.03990.13480.06560.267535.506518.032938.5573
111.2872-0.6513-0.29761.59180.68612.0005-0.067-0.01820.0678-0.23930.5021-0.26720.4283-0.0618-0.21730.3473-0.21280.01860.1485-0.03240.323143.825515.712618.3452
123.13541.1752-1.64534.7179-4.00223.5471-0.2033-0.28850.50230.01150.2589-0.2863-1.30060.41690.19060.7219-0.1564-0.01270.2622-0.19110.568550.668915.570116.5341
133.08510.4378-0.21460.1682-0.34072.0091-0.1032-0.15580.01790.01950.12010.1416-0.77110.1464-0.11980.6099-0.0019-0.1280.3588-0.06990.433545.277412.283212.5509
141.7662-0.4605-0.66361.668-1.18621.4296-0.0574-0.21041.1345-0.03720.2365-0.6898-0.67690.9171-0.00710.8883-0.3264-0.07140.5297-0.04640.619254.834718.64694.1383
152.1593-0.1366-0.53982.0881-0.68320.3793-0.4283-0.22410.2417-0.38460.5553-0.6924-0.62650.909-0.14720.6595-0.3164-0.06260.7275-0.24080.64459.082713.690811.9532
162.65610.1841-1.47452.49380.28015.00830.0861-0.084-0.0014-0.3035-0.03980.74760.5596-0.7491-0.09250.289-0.0149-0.23720.4211-0.02020.636413.384822.30821.766
171.3913-1.3564-1.33582.16551.77472.47490.33350.0172-0.1766-0.4145-0.15820.1839-0.2152-0.4092-0.11570.2946-0.0524-0.14310.28350.03570.282824.485923.91217.2897
181.7878-0.8647-0.58373.17781.19192.2266-0.2551-0.1563-0.0863-0.34530.16560.0133-0.3325-0.00590.0230.576-0.0719-0.04640.2393-0.12580.339242.77833.92080.9943
195.26050.5910.52973.1085-0.77263.746-0.0256-0.5386-0.3747-0.3830.19471.10430.2335-0.7394-0.01030.4005-0.0869-0.09620.35980.11880.580923.048551.14363.8263
203.922-0.3828-2.65482.5299-0.17453.14430.14-0.1273-0.31310.20810.17410.9499-0.3421-0.3905-0.47990.5345-0.03820.34010.1530.47150.173427.09957.85355.6529
211.13350.2976-0.7780.32420.28141.5067-0.0114-0.0364-0.20320.0380.34320.82710.1624-0.31940.67870.49390.0559-0.15530.20320.29040.65129.0742.463412.1205
222.0919-0.83731.98295.4804-1.23311.9116-0.6326-0.67490.00750.75130.3310.8706-0.6112-0.3177-0.18120.6240.12440.10980.29010.00720.444233.196751.497118.1742
232.97710.33980.07294.67940.80734.28220.04910.2421-0.40680.43770.0186-0.2828-0.34490.3982-0.17250.2785-0.01520.00550.06580.04950.17937.892651.89331.6912
242.66030.0313-0.8373.8497-0.65613.333-0.04970.1066-0.1639-0.03470.3291-0.10370.03980.0379-0.13670.2233-0.0656-0.00370.11370.03520.25739.114550.7598-1.1796
253.0506-0.10180.25212.4129-0.15493.33160.20070.32390.1434-0.5945-0.0908-0.3283-0.65750.4151-0.12840.5289-0.02560.08410.2348-0.050.199644.132659.0329-12.3592
263.076-1.6364-1.55345.69532.83265.7818-0.0886-0.31070.58960.70810.29410.2706-0.7577-0.0812-0.03350.6782-0.09020.01310.00360.06580.4430.041256.648312.1121
272.44970.30760.92191.9983-0.18711.48170.1217-0.0071-0.3097-0.20940.24020.05160.20190.047-0.1370.20240.02870.00410.1041-0.03610.148445.762830.942222.9209
282.5283-1.63310.13642.1789-0.06222.06910.09140.19460.2576-0.17180.013-0.3109-0.0540.2755-0.16050.18140.01140.04540.1003-0.00950.172553.453638.256421.7916
291.5378-0.23460.34741.0767-0.78731.73280.147-0.0571-0.05790.4785-0.12460.0557-0.27930.2146-0.03770.2974-0.010.03540.0362-0.00250.250551.244231.289438.2845
302.0584-1.06370.45832.01920.28093.51560.1298-0.1641-0.3185-0.0006-0.04330.47390.5811-0.3188-0.02910.2538-0.0289-0.00380.31720.12970.487952.761520.835755.0345
311.7765-0.13430.03731.2692-0.58014.0934-0.3361-0.36910.7133-0.17790.07880.1971-0.78010.0796-0.44620.55030.0187-0.09030.021-0.15110.473945.713757.309636.458
322.87170.02140.13253.5491-0.97623.8979-0.08210.03580.02670.33650.1070.2816-0.4606-0.423-0.05440.24590.08260.03010.2072-0.03370.123938.262447.45236.0181
331.7786-0.23441.05180.7041-0.84672.4375-0.0436-0.24510.18850.0548-0.0388-0.0824-0.417-0.10470.10920.35410.05170.01940.2117-0.09640.231244.504750.820841.7827
346.3274-3.1117-0.02083.41471.31271.85130.5977-0.1367-0.3162-0.188-0.3878-0.21050.1670.1267-0.1550.3193-0.0595-0.02750.25590.020.281259.772728.569561.665
353.2741-0.86593.72040.4012-1.00354.22740.1784-0.21410.4811-0.0377-0.298-0.5301-0.39230.6867-0.06920.22930.0037-0.07160.47150.0380.399269.447536.784265.205
361.8725-2.0277-0.19052.2827-0.25342.51741.13770.3012-0.2674-0.2587-0.77050.1301-0.056-0.1067-0.27630.348-0.0478-0.00270.3146-0.01580.421352.837936.786255.8665
374.0997-2.14630.34833.0851-0.19192.411-0.2267-0.7276-0.1980.63420.2121-0.2703-0.0580.281-0.14210.30570.0382-0.05550.41330.0180.338765.650931.501665.9058
383.31380.09410.87282.64931.05555.0222-0.0806-0.17790.4114-0.2287-0.0010.409-0.3516-2.3753-0.08450.59310.3126-0.0781.01910.01210.44528.401954.5267-36.027
392.35420.9813-0.32324.75443.82493.682-0.33540.1496-0.90570.3142-0.12910.22820.18710.03080.21920.48930.21230.03670.8208-0.13520.230639.584650.3061-36.9406
401.41920.8781.231.4259-0.56053.0471-0.02980.4480.0279-0.1269-0.0050.113-1.2633-0.9304-0.03820.75260.33980.02390.81150.00170.233936.446658.0494-37.2396
412.64870.4554-0.40231.34990.11386.87180.20270.0808-0.3159-0.13620.1643-0.1980.4524-0.8955-0.14250.38450.15570.01580.5535-0.05760.247137.993350.4158-31.6518
425.4668-0.337-3.71793.4890.71666.9115-0.6979-0.40390.55540.36510.2408-0.3892-0.5073-0.36760.4640.5491-0.0178-0.05270.8333-0.4070.7626.283652.987294.4418
434.60530.30481.97615.66923.13772.7834-0.48770.05540.9732-0.6113-0.5395-0.7721-1.40870.73080.7370.35940.0032-0.06380.62890.00990.510210.697846.631284.4724
444.9526-0.08031.14464.6705-0.16454.2825-0.3285-0.77820.11740.5912-0.0027-0.3103-0.21580.13170.37330.24910.0356-0.01070.6267-0.0360.36274.893842.707493.2615
450.351-0.5874-0.29511.0340.93683.0345-0.0232-0.54070.18550.28410.3543-0.3247-0.50460.9746-0.23910.249-0.08760.0520.9169-0.13450.386612.538943.351388.9513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 332 through 364 )A332 - 364
2X-RAY DIFFRACTION2chain 'A' and (resid 365 through 380 )A365 - 380
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 393 )A381 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 421 )A394 - 421
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 516 )A422 - 516
6X-RAY DIFFRACTION6chain 'A' and (resid 517 through 528 )A517 - 528
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 39 )B0 - 39
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 52 )B40 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 73 )B53 - 73
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 100 )B74 - 100
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 147 )B101 - 147
12X-RAY DIFFRACTION12chain 'B' and (resid 148 through 161 )B148 - 161
13X-RAY DIFFRACTION13chain 'B' and (resid 162 through 181 )B162 - 181
14X-RAY DIFFRACTION14chain 'B' and (resid 182 through 204 )B182 - 204
15X-RAY DIFFRACTION15chain 'B' and (resid 205 through 219 )B205 - 219
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 38 )C1 - 38
17X-RAY DIFFRACTION17chain 'C' and (resid 39 through 128 )C39 - 128
18X-RAY DIFFRACTION18chain 'C' and (resid 129 through 219 )C129 - 219
19X-RAY DIFFRACTION19chain 'E' and (resid 333 through 349 )E333 - 349
20X-RAY DIFFRACTION20chain 'E' and (resid 350 through 364 )E350 - 364
21X-RAY DIFFRACTION21chain 'E' and (resid 365 through 375 )E365 - 375
22X-RAY DIFFRACTION22chain 'E' and (resid 376 through 393 )E376 - 393
23X-RAY DIFFRACTION23chain 'E' and (resid 394 through 409 )E394 - 409
24X-RAY DIFFRACTION24chain 'E' and (resid 410 through 451 )E410 - 451
25X-RAY DIFFRACTION25chain 'E' and (resid 452 through 506 )E452 - 506
26X-RAY DIFFRACTION26chain 'E' and (resid 507 through 527 )E507 - 527
27X-RAY DIFFRACTION27chain 'H' and (resid 0 through 32 )H0 - 32
28X-RAY DIFFRACTION28chain 'H' and (resid 33 through 91 )H33 - 91
29X-RAY DIFFRACTION29chain 'H' and (resid 92 through 138 )H92 - 138
30X-RAY DIFFRACTION30chain 'H' and (resid 139 through 219 )H139 - 219
31X-RAY DIFFRACTION31chain 'L' and (resid 1 through 38 )L1 - 38
32X-RAY DIFFRACTION32chain 'L' and (resid 39 through 67 )L39 - 67
33X-RAY DIFFRACTION33chain 'L' and (resid 68 through 119 )L68 - 119
34X-RAY DIFFRACTION34chain 'L' and (resid 120 through 149 )L120 - 149
35X-RAY DIFFRACTION35chain 'L' and (resid 150 through 161 )L150 - 161
36X-RAY DIFFRACTION36chain 'L' and (resid 162 through 178 )L162 - 178
37X-RAY DIFFRACTION37chain 'L' and (resid 179 through 219 )L179 - 219
38X-RAY DIFFRACTION38chain 'F' and (resid 1 through 32 )F1 - 32
39X-RAY DIFFRACTION39chain 'F' and (resid 33 through 52 )F33 - 52
40X-RAY DIFFRACTION40chain 'F' and (resid 53 through 99 )F53 - 99
41X-RAY DIFFRACTION41chain 'F' and (resid 100 through 127 )F100 - 127
42X-RAY DIFFRACTION42chain 'D' and (resid 1 through 25 )D1 - 25
43X-RAY DIFFRACTION43chain 'D' and (resid 26 through 39 )D26 - 39
44X-RAY DIFFRACTION44chain 'D' and (resid 40 through 91 )D40 - 91
45X-RAY DIFFRACTION45chain 'D' and (resid 92 through 127 )D92 - 127

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more