PDB-9hpq: Peptide-substrate-binding (PSB) domain of human type I collagen p...

ID or keywords:

Entry

Database: PDB / ID: 9hpq

Title

Peptide-substrate-binding (PSB) domain of human type I collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Arg-Gly-Pro-Pro-Gly.

Components

Prolyl 4-hydroxylase subunit alpha-1
Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

Keywords

PROTEIN BINDING / collagen / tetratricopeptide / extracellular matrix

Function / homology

Function and homology information

procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase complex / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / collagen fibril organization / L-ascorbic acid binding / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.17 Å

Authors

Sulu, R. / Rahman, M.M. / Wierenga, R.K. / Koski, M.K.

Funding support

Finland, 2items

Citation

Journal: Proteins / Year: 2025
Title: Binding Differences of the Peptide-Substrate-Binding Domain of Collagen Prolyl 4-Hydroxylases I and II for Proline- and Hydroxyproline-Rich Peptides.
Authors: Rahman, M.M. / Sulu, R. / Adediran, B. / Tu, H. / Salo, A.M. / Murthy, S. / Myllyharju, J. / Wierenga, R.K. / Koski, M.K.

History

Deposition	Dec 16, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hpq.cif.gz	424.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9hpq.ent.gz	296.6 KB	Display	PDB format
PDBx/mmJSON format	9hpq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hpq_validation.pdf.gz	519.7 KB	Display	wwPDB validaton report
Full document	9hpq_full_validation.pdf.gz	526.6 KB	Display
Data in XML	9hpq_validation.xml.gz	23.2 KB	Display
Data in CIF	9hpq_validation.cif.gz	30.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hp/9hpq ftp://data.pdbj.org/pub/pdb/validation_reports/hp/9hpq	HTTPS FTP

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Related structure data

Related structure data	9hreC 9ht8C 9htdC 1tjc 2v5f 4bt8 4bta 4btb C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (5) #4 - Apr 2000 Collagen similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (3) #166 - Oct 2013 Proteasome similarity (3) #230 - Feb 2019 Initiation Factor eIF4E similarity (3) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Prolyl 4-hydroxylase subunit alpha-1

B: Prolyl 4-hydroxylase subunit alpha-1

C: Prolyl 4-hydroxylase subunit alpha-1

D: Prolyl 4-hydroxylase subunit alpha-1

E: Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

F: Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

G: Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

hetero molecules

54.4 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Prolyl 4-hydroxylase subunit alpha-1

E: Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

hetero molecules

defined by author&software
Evidence: light scattering, SEC-MALS confirms that the PSB-I is monomer in the solution
13.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Prolyl 4-hydroxylase subunit alpha-1

F: Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

hetero molecules

defined by author&software
13.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Prolyl 4-hydroxylase subunit alpha-1

hetero molecules

defined by author&software
12.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Prolyl 4-hydroxylase subunit alpha-1

G: Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

hetero molecules

defined by author&software
14 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.418, 86.315, 91.132
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PHE	PHE	HIS	HIS	A	A	144 - 242	3 - 101
2	1	1	PHE	PHE	HIS	HIS	B	B	144 - 242	3 - 101
3	2	2	PHE	PHE	GLU	GLU	A	A	144 - 238	3 - 97
4	2	2	PHE	PHE	GLU	GLU	C	C	144 - 238	3 - 97
5	3	3	PHE	PHE	HIS	HIS	A	A	144 - 243	3 - 102
6	3	3	PHE	PHE	HIS	HIS	D	D	144 - 243	3 - 102
7	4	4	PHE	PHE	GLU	GLU	B	B	144 - 238	3 - 97
8	4	4	PHE	PHE	GLU	GLU	C	C	144 - 238	3 - 97
9	5	5	SER	SER	HIS	HIS	B	B	143 - 242	2 - 101
10	5	5	SER	SER	HIS	HIS	D	D	143 - 242	2 - 101
11	6	6	PHE	PHE	GLU	GLU	C	C	144 - 238	3 - 97
12	6	6	PHE	PHE	GLU	GLU	D	D	144 - 238	3 - 97

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFG

#1: Protein	Prolyl 4-hydroxylase subunit alpha-1 / 4-PH alpha-1 / Procollagen-proline / 2-oxoglutarate-4-dioxygenase subunit alpha-1 Mass: 12404.898 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: His-tag in the C-terminus. / Source: (gene. exp.) Homo sapiens (human) / Gene: P4HA1, P4HA / Production host: Escherichia coli (E. coli) References: UniProt: P13674, procollagen-proline 4-dioxygenase
#2: Protein/peptide	Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY Mass: 831.938 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: The first two prolines, and the last glycine are not built to the model because of the missing electron density. Source: (synth.) Homo sapiens (human)

#1: Protein

Prolyl 4-hydroxylase subunit alpha-1 / 4-PH alpha-1 / Procollagen-proline / 2-oxoglutarate-4-dioxygenase subunit alpha-1

Mass: 12404.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His-tag in the C-terminus. / Source: (gene. exp.)

Homo sapiens (human) / Gene: P4HA1, P4HA / Production host:

Escherichia coli (E. coli)
References: UniProt: P13674, procollagen-proline 4-dioxygenase

#2: Protein/peptide

Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY

Mass: 831.938 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The first two prolines, and the last glycine are not built to the model because of the missing electron density.
Source: (synth.)

Homo sapiens (human)

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Non-polymers , 5 types, 153 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#6: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 55.02 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% MPD, 50 mM MgCl2, 50 mM KCl, 100 mM MOPS / Temp details: cold room, fluctuates between 277 and 279 K.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 29, 2017 / Details: CRL
Radiation	Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 2.17→49.88 Å / Num. obs: 34940 / % possible obs: 99.6 % / Redundancy: 4.7 % / B_iso Wilson estimate: 52.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.058 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.17→2.25 Å / Redundancy: 4.7 % / R_merge(I) obs: 1.412 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3373 / CC_1/2: 0.482 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.17→49.88 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.943 / SU B: 15.177 / SU ML: 0.183 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2499	1726	4.953 %	Random selection
R_work	0.225	33120	-	-
all	0.226	-	-	-
obs	-	34846	99.387 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 63.77 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.606 Å²	-0 Å²	-0 Å²
2-	-	-1.1 Å²	-0 Å²
3-	-	-	1.706 Å²

Refinement step

Cycle: LAST / Resolution: 2.17→49.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3453	0	149	130	3732

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3689
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3440
X-RAY DIFFRACTION	r_angle_refined_deg	1.525	1.868	4983
X-RAY DIFFRACTION	r_angle_other_deg	0.522	1.773	7963
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.942	5	422
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.461	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.195	10	624
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.629	10	189
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	535
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4126
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	774
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	809
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.175	0.2	2811
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	1788
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	1888
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	108
X-RAY DIFFRACTION	r_metal_ion_refined	0.078	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.138	0.2	33
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	103
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.178	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	2.432	2.811	1712
X-RAY DIFFRACTION	r_mcbond_other	2.432	2.81	1711
X-RAY DIFFRACTION	r_mcangle_it	3.656	5.02	2114
X-RAY DIFFRACTION	r_mcangle_other	3.655	5.02	2115
X-RAY DIFFRACTION	r_scbond_it	4.046	3.589	1977
X-RAY DIFFRACTION	r_scbond_other	4.033	3.587	1975
X-RAY DIFFRACTION	r_scangle_it	6.239	6.362	2865
X-RAY DIFFRACTION	r_scangle_other	6.238	6.362	2866
X-RAY DIFFRACTION	r_lrange_it	9.373	34.18	4159
X-RAY DIFFRACTION	r_lrange_other	9.372	34.131	4151
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.092	0.05	3287
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.098	0.05	3098
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.093	0.05	3327
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.104	0.05	3076
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.09	0.05	3309
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.112	0.05	3060

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09226	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09226	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09751	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09751	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09305	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.09305	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.10372	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.10372	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.09009	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.09009	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.11247	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.11247	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.17-2.226	0.347	155	0.346	2359	X-RAY DIFFRACTION	99.5644
2.226-2.287	0.387	151	0.338	2304	X-RAY DIFFRACTION	98.7133
2.287-2.353	0.309	135	0.293	2292	X-RAY DIFFRACTION	99.6305
2.353-2.426	0.326	128	0.276	2204	X-RAY DIFFRACTION	99.7434
2.426-2.505	0.242	98	0.264	2183	X-RAY DIFFRACTION	99.8687
2.505-2.593	0.268	89	0.244	2117	X-RAY DIFFRACTION	99.6837
2.593-2.69	0.325	94	0.249	2042	X-RAY DIFFRACTION	99.7199
2.69-2.8	0.297	102	0.245	1949	X-RAY DIFFRACTION	99.8054
2.8-2.924	0.233	102	0.234	1874	X-RAY DIFFRACTION	99.7476
2.924-3.066	0.277	79	0.233	1816	X-RAY DIFFRACTION	99.7894
3.066-3.231	0.272	93	0.234	1693	X-RAY DIFFRACTION	99.6096
3.231-3.426	0.25	89	0.223	1631	X-RAY DIFFRACTION	99.5947
3.426-3.662	0.268	70	0.215	1527	X-RAY DIFFRACTION	99.131
3.662-3.953	0.226	66	0.195	1433	X-RAY DIFFRACTION	98.3596
3.953-4.328	0.218	71	0.185	1327	X-RAY DIFFRACTION	99.3603
4.328-4.834	0.202	67	0.168	1192	X-RAY DIFFRACTION	99.2902
4.834-5.573	0.233	43	0.229	1079	X-RAY DIFFRACTION	99.38
5.573-6.805	0.293	52	0.259	919	X-RAY DIFFRACTION	99.0816
6.805-9.535	0.277	25	0.207	738	X-RAY DIFFRACTION	98.1982
9.535-49.88	0.112	17	0.247	441	X-RAY DIFFRACTION	95.2183

Refinement TLS params.

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

ID	L11 (°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)
1	3.1735	-0.0357	-0.9901	4.3204	1.118	1.5454	0.4146	-0.2306	0.0904	0.3201	-0.439	0.1673	0.0369	0.0598	0.0245	0.4596	-0.1242	0.02	0.4896	0.0032	0.0108	-24.655	-3.201	-12.1076
2	2.9864	0.3295	0.321	4.2445	0.493	2.3591	0.0383	-0.1371	0.22	0.4854	-0.0268	-0.1113	-0.1214	0.1793	-0.0115	0.1923	0.0072	-0.0119	0.3252	0.0098	0.0761	-26.1911	8.4875	-33.8427
3	3.0591	-0.8641	1.2281	4.4323	0.2906	2.4073	-0.4912	-0.0284	-0.118	0.2042	0.3494	0.1819	-0.2811	-0.6182	0.1418	0.5261	0.1091	0.0165	0.6267	-0.07	0.0267	-7.1283	28.2253	-11.9313
4	3.5022	-0.6859	2.5825	2.871	-1.4531	3.0459	-0.0967	-0.396	0.0586	0.2104	0.0775	0.0512	0.2339	-0.0671	0.0192	0.3079	0.0073	0.0377	0.3317	-0.0305	0.0434	2.6396	26.1414	-33.9836
5	6.0443	-3.0987	3.8787	15.3639	-0.634	2.6283	-0.1293	0.1267	-0.2318	-0.3062	0.4488	-1.3647	-0.1072	0.1708	-0.3195	0.4416	-0.0628	0.0323	0.5391	-0.0198	0.4241	-17.1266	-6.4984	-4.1507
6	0.7218	0.4078	-0.8369	20.4971	-1.3132	1.5717	0.0221	0.088	0.2289	-0.1447	0.2024	-0.7986	-0.1803	0.1128	-0.2246	0.3439	-0.0057	-0.0243	0.4349	0.0007	0.4644	-19.5258	16.8873	-41.2284
7	4.3614	-5.888	0.339	12.9653	1.8348	1.0887	0.1941	0.073	-0.0424	-0.0547	-0.0586	-0.2927	0.1946	0.035	-0.1355	0.5332	0.0125	0.0634	0.4392	0.0289	0.3586	6.0357	18.2302	-41.4798
8	1.4682	-0.1594	-0.5116	0.83	-0.1441	0.2449	-0.146	0.0358	-0.0455	-0.2806	0.054	-0.1779	0.0383	-0.0167	0.0919	0.5475	0.0077	-0.0594	0.717	-0.006	0.3871	-13.8584	19.3239	-32.9281

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	144 - 245
2	X-RAY DIFFRACTION	2	ALL	Bp	143 - 243
3	X-RAY DIFFRACTION	3	ALL	Cp	144 - 239
4	X-RAY DIFFRACTION	4	ALL	Dp	143 - 244
5	X-RAY DIFFRACTION	5	ALL	Ep	4 - 9
6	X-RAY DIFFRACTION	6	ALL	Fp	1 - 8
7	X-RAY DIFFRACTION	7	ALL	Gp	3 - 8
8	X-RAY DIFFRACTION	8	ALL	Np	1 - 9

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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFG

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Non-polymers , 5 types, 153 molecules

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-Protein / Protein/peptide , 2 types, 7 molecules ABCDEFG

-Non-polymers , 5 types, 153 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

-
This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

-
Links

-
Assembly

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Components

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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFG

-
Non-polymers , 5 types, 153 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi