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

ID or keywords:

Entry

Database: PDB / ID: 9hre

Title

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

Components

Prolyl 4-hydroxylase subunit alpha-1
Synthetic peptide PRO-HYP-GLY-PRO-ALA-GLY-PRO-HYP-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: 2.05 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 18, 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	9hre.cif.gz	420.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9hre.ent.gz	287 KB	Display	PDB format
PDBx/mmJSON format	9hre.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hre_validation.pdf.gz	526.7 KB	Display	wwPDB validaton report
Full document	9hre_full_validation.pdf.gz	533.3 KB	Display
Data in XML	9hre_validation.xml.gz	23.7 KB	Display
Data in CIF	9hre_validation.cif.gz	30.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/9hre ftp://data.pdbj.org/pub/pdb/validation_reports/hr/9hre	HTTPS FTP

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Related structure data

Related structure data	9hpqC 9ht8C 9htdC 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-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY

F: Synthetic peptide PRO-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY

G: Synthetic peptide PRO-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY

hetero molecules

54.3 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-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY

hetero molecules

defined by author
Evidence: light scattering, SEC-MALS experiments confirmed PSB-I being a 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-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY

hetero molecules

defined by author
13.7 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
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-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.041, 85.561, 92.506
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	SER	SER	GLU	GLU	A	A	143 - 240	2 - 99
4	2	2	SER	SER	GLU	GLU	C	C	143 - 240	2 - 99
5	3	3	SER	SER	HIS	HIS	A	A	143 - 243	2 - 102
6	3	3	SER	SER	HIS	HIS	D	D	143 - 243	2 - 102
7	4	4	PHE	PHE	GLU	GLU	B	B	144 - 240	3 - 99
8	4	4	PHE	PHE	GLU	GLU	C	C	144 - 240	3 - 99
9	5	5	PHE	PHE	HIS	HIS	B	B	144 - 242	3 - 101
10	5	5	PHE	PHE	HIS	HIS	D	D	144 - 242	3 - 101
11	6	6	SER	SER	GLU	GLU	C	C	143 - 240	2 - 99
12	6	6	SER	SER	GLU	GLU	D	D	143 - 240	2 - 99

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-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY Mass: 777.822 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: The hydroxyprolines, 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-HYP-GLY-PRO-ALA-GLY-PRO-HYP-GLY

Mass: 777.822 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The hydroxyprolines, 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, 152 molecules

#3: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.78 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% MPD, 48 mM MgCl2, 50 mM KCl, 100 mM MOPS, 5 mM peptide (POG-PAG-POG) 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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2018 / Details: Toroidal mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.05→92.51 Å / Num. obs: 40436 / % possible obs: 98.8 % / Redundancy: 6.6 % / B_iso Wilson estimate: 46.01 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.03 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.05→2.11 Å / Redundancy: 6.8 % / R_merge(I) obs: 1.65 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3046 / CC_1/2: 0.468 / R_pim(I) all: 0.676 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→62.89 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.955 / SU B: 9.511 / SU ML: 0.119 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.218	1965	4.864 %	Random selection
R_work	0.1972	38438	-	-
all	0.198	-	-	-
obs	-	40403	98.52 %	-

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: 60.834 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.25 Å²	0 Å²	0 Å²
2-	-	1.176 Å²	0 Å²
3-	-	-	-2.426 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→62.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3466	0	149	129	3744

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	3687
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3416
X-RAY DIFFRACTION	r_angle_refined_deg	1.686	1.863	4981
X-RAY DIFFRACTION	r_angle_other_deg	0.565	1.767	7916
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.99	5	422
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.872	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.504	10	617
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.276	10	185
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	538
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4103
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	757
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	853
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2857
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	1812
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1930
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	133
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.055	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.059	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.14	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.151	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.147	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	4.203	4.64	1724
X-RAY DIFFRACTION	r_mcbond_other	4.204	4.636	1723
X-RAY DIFFRACTION	r_mcangle_it	5.672	8.235	2128
X-RAY DIFFRACTION	r_mcangle_other	5.674	8.238	2129
X-RAY DIFFRACTION	r_scbond_it	6.489	5.617	1963
X-RAY DIFFRACTION	r_scbond_other	6.488	5.618	1964
X-RAY DIFFRACTION	r_scangle_it	9.996	9.947	2851
X-RAY DIFFRACTION	r_scangle_other	9.994	9.947	2852
X-RAY DIFFRACTION	r_lrange_it	12.125	51.014	4236
X-RAY DIFFRACTION	r_lrange_other	12.11	50.566	4217
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.108	0.05	3282
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.091	0.05	3251
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.108	0.05	3310
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.122	0.05	3139
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.085	0.05	3317
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.121	0.05	3156

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	0.10788	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10788	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09107	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09107	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10783	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.10783	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.12168	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.12168	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.08544	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.08544	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.12109	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.12109	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 (%)
2.051-2.104	0.32	131	0.32	2759	X-RAY DIFFRACTION	96.7202
2.104-2.162	0.272	126	0.272	2722	X-RAY DIFFRACTION	98.6491
2.162-2.224	0.269	140	0.235	2666	X-RAY DIFFRACTION	98.6986
2.224-2.292	0.235	130	0.23	2574	X-RAY DIFFRACTION	98.7582
2.292-2.368	0.286	124	0.214	2529	X-RAY DIFFRACTION	98.1139
2.368-2.451	0.218	145	0.197	2414	X-RAY DIFFRACTION	98.8412
2.451-2.543	0.242	115	0.194	2339	X-RAY DIFFRACTION	99.0315
2.543-2.647	0.231	125	0.187	2239	X-RAY DIFFRACTION	98.5822
2.647-2.764	0.248	108	0.195	2210	X-RAY DIFFRACTION	99.5277
2.764-2.899	0.217	107	0.19	2088	X-RAY DIFFRACTION	98.7404
2.899-3.055	0.249	119	0.203	1976	X-RAY DIFFRACTION	98.3568
3.055-3.24	0.213	105	0.183	1879	X-RAY DIFFRACTION	99.1504
3.24-3.463	0.237	96	0.19	1776	X-RAY DIFFRACTION	99.1001
3.463-3.739	0.209	100	0.189	1667	X-RAY DIFFRACTION	99.3255
3.739-4.095	0.203	92	0.177	1519	X-RAY DIFFRACTION	99.1995
4.095-4.576	0.192	66	0.165	1411	X-RAY DIFFRACTION	98.9283
4.576-5.279	0.127	51	0.16	1249	X-RAY DIFFRACTION	98.0392
5.279-6.454	0.276	32	0.233	1075	X-RAY DIFFRACTION	97.4472
6.454-9.08	0.2	28	0.218	857	X-RAY DIFFRACTION	97.6821
9.08-62.89	0.234	25	0.228	489	X-RAY DIFFRACTION	93.4545

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	0.2812	0.1174	0.1894	0.3609	-0.3665	0.7979	0.0617	-0.0263	-0.0517	0.018	-0.0208	-0.0431	0.0333	-0.0433	-0.0409	0.091	-0.0022	-0.0099	0.1098	-0.0005	0.0871	24.8179	2.6648	33.7031
2	0.2408	0.2468	-0.0156	0.5206	-0.235	0.3632	0.0621	0.0027	-0.0023	0.007	-0.0038	-0.0284	0.0063	-0.0827	-0.0583	0.093	0.0094	-0.0088	0.1109	-0.0128	0.0996	25.8715	-8.773	11.9292
3	0.1676	0.1574	-0.0443	0.247	-0.2734	0.6152	-0.055	0.0467	-0.0201	0.0073	0.0355	-0.0056	-0.1022	0.0719	0.0196	0.1225	-0.0157	-0.0102	0.1165	0.013	0.0972	7.1911	-28.5003	34.1062
4	0.3999	-0.0202	-0.3752	0.1481	0.1641	0.5056	0.0551	0.0071	-0.0723	-0.008	-0.0249	-0.079	-0.086	-0.0374	-0.0303	0.1191	-0.0062	-0.0126	0.0917	0.0049	0.0999	-2.42	-26.1524	11.8006
5	6.8789	-8.2069	1.5369	19.6979	-11.1891	9.179	-0.3834	-0.2072	0.3957	0.8089	0.2008	-0.553	-0.392	0.0214	0.1826	0.1436	-0.0097	-0.0504	0.119	0.0026	0.0908	18.6417	6.9869	40.2343
6	3.31	1.7608	0.2305	0.9983	0.3524	1.0034	0.0857	0.4563	-0.236	0.1003	0.1264	-0.1765	0.0093	-0.2772	-0.2121	0.1558	-0.0154	-0.0421	0.1775	-0.0043	0.1177	19.9175	-16.2391	4.4648
7	4.1076	-4.4323	-3.0469	6.0381	4.2944	3.0682	-0.1808	-0.209	0.0326	-0.1806	0.1671	0.0346	-0.1623	0.1111	0.0137	0.153	0.018	0.0031	0.1275	0.0295	0.0599	-4.5674	-19.447	4.168
8	0.0614	-0.0369	-0.0522	0.4187	-0.0496	0.0633	-0.0194	-0.0599	-0.0579	-0.0252	-0.0116	-0.0455	-0.0165	0.0299	0.031	0.0213	-0.0209	-0.0284	0.2814	-0.0113	0.0996	7.9047	-22.8397	16.6914

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	143 - 245
2	X-RAY DIFFRACTION	2	ALL	Bp	144 - 243
3	X-RAY DIFFRACTION	3	ALL	Cp	143 - 241
4	X-RAY DIFFRACTION	4	ALL	Dp	143 - 244
5	X-RAY DIFFRACTION	5	ALL	Ep	4 - 8
6	X-RAY DIFFRACTION	6	ALL	Fp	1 - 9
7	X-RAY DIFFRACTION	7	ALL	Gp	3 - 9
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, 152 molecules

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

-Non-polymers , 5 types, 152 molecules

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-Experimental details

-Experiment

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-Data collection

-Processing

+About Yorodumi

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

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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

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Structure viewers

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Viewer log

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This page

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This web site

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Components

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

-
Non-polymers , 5 types, 152 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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

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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